diff --git a/.changeset/olive-rats-kick.md b/.changeset/olive-rats-kick.md
new file mode 100644
index 000000000..30ab43f81
--- /dev/null
+++ b/.changeset/olive-rats-kick.md
@@ -0,0 +1,5 @@
+---
+'@openfn/cli': minor
+---
+
+Remove renamed/deleted workflows or steps during checkout
diff --git a/.claude/command-refactor.md b/.claude/command-refactor.md
index ea6930782..9359ee505 100644
--- a/.claude/command-refactor.md
+++ b/.claude/command-refactor.md
@@ -13,6 +13,7 @@ Use `src/projects/list.ts` as the reference pattern for all refactored commands.
 Create a new file in `src/projects/<command-name>.ts` that consolidates all the existing command files.
 
 **Key elements:**
+
 - Import `yargs`, `ensure`, `build`, `Logger`, and options from `../options`
 - Define a `<CommandName>Options` type that picks required fields from `Opts`
 - Create an `options` array with the required options (e.g., `[o.workflow, o.workspace, o.workflowMappings]`)
@@ -24,6 +25,7 @@ Create a new file in `src/projects/<command-name>.ts` that consolidates all the
 - Export a named `handler` function that takes `(options: <CommandName>Options, logger: Logger)`
 
 **Example structure:**
+
 ```typescript
 import yargs from 'yargs';
 import { Workspace } from '@openfn/project';
@@ -88,23 +90,26 @@ export const projectsCommand = {
 Make three changes:
 
 **a) Remove the old import** (if it exists):
+
 ```typescript
 // Remove: import commandName from './<command>/handler';
 ```
 
 **b) Add to CommandList type:**
+
 ```typescript
 export type CommandList =
   | 'apollo'
   // ...
   | 'project-list'
   | 'project-version'
-  | 'project-<command-name>'  // Add this line
+  | 'project-<command-name>' // Add this line
   | 'test'
   | 'version';
 ```
 
 **c) Add to handlers object:**
+
 ```typescript
 const handlers = {
   // ...
@@ -121,6 +126,7 @@ If the old command was referenced elsewhere in the handlers object (like `projec
 ### 5. Delete the Old Command Folder
 
 Remove the old command directory:
+
 ```bash
 rm -rf packages/cli/src/<command-name>
 ```
@@ -142,6 +148,7 @@ import checkoutCommand from './checkout/command';
 ```
 
 The command will be registered with yargs:
+
 ```typescript
 .command(projectsCommand)
 .command(mergeCommand)  // Top-level alias
@@ -159,18 +166,21 @@ This is different from the `install`/`repo install` pattern, where both entries
 ## Common Patterns
 
 ### Options to Use
+
 - Always include `o.workspace` for project-related commands
 - Use `o.workflow` for workflow-specific operations
 - Include `o.json` if the command supports JSON output
 - Include `o.log` for commands that need detailed logging
 
 ### Handler Pattern
+
 - Use `new Workspace(options.workspace)` to access the workspace
 - Check `workspace.valid` before proceeding
-- Use `workspace.getActiveProject()` to get the current project
+- Use `workspace.getTrackedProject()` to get the current project
 - Use appropriate logger methods: `logger.info()`, `logger.error()`, `logger.success()`
 
 ### Testing Pattern
+
 If the old command has tests, they need to be refactored:
 
 1. **Create new test file**: Move from `test/<command>/handler.test.ts` to `test/projects/<command>.test.ts`
@@ -181,6 +191,7 @@ If the old command has tests, they need to be refactored:
 4. **Delete old test folder**: Remove `test/<command>` directory
 
 **Example changes:**
+
 ```typescript
 // Before:
 import mergeHandler from '../../src/merge/handler';
@@ -194,6 +205,7 @@ await mergeHandler({ command: 'project-merge', ... }, logger);
 ## Checklist
 
 ### Basic Refactoring
+
 - [ ] Create new file in `src/projects/<command-name>.ts`
 - [ ] Define `<CommandName>Options` type
 - [ ] Export default command object with `ensure('project-<command-name>', options)`
@@ -206,6 +218,7 @@ await mergeHandler({ command: 'project-merge', ... }, logger);
 - [ ] Delete old command folder
 
 ### Testing (if applicable)
+
 - [ ] Create new test file in `test/projects/<command-name>.test.ts`
 - [ ] Update import to use `{ handler } from '../../src/projects/<command-name>'`
 - [ ] Update all `command: '<command>'` to `command: 'project-<command>'` in test cases
@@ -213,6 +226,7 @@ await mergeHandler({ command: 'project-merge', ... }, logger);
 - [ ] Run tests to verify they pass
 
 ### Additional Steps for Top-Level Aliasing
+
 - [ ] Import command directly in `src/cli.ts` (e.g., `import mergeCommand from './projects/merge'`)
 - [ ] Register the imported command with `.command(mergeCommand)`
 - [ ] Verify NO duplicate entries in `src/commands.ts` - only `project-<command-name>` should exist, not `<command-name>`
diff --git a/packages/cli/src/projects/checkout.ts b/packages/cli/src/projects/checkout.ts
index 5ae52a2f7..c81351a85 100644
--- a/packages/cli/src/projects/checkout.ts
+++ b/packages/cli/src/projects/checkout.ts
@@ -46,8 +46,7 @@ export const handler = async (options: CheckoutOptions, logger?: Logger) => {
   // TODO: try to retain the endpoint for the projects
   const { project: _, ...config } = workspace.getConfig() as any;
 
-  const currentProject = workspace.getActiveProject();
-
+  const currentProject = await workspace.getCheckedOutProject();
   // get the project
   let switchProject;
   if (/\.(yaml|json)$/.test(projectIdentifier)) {
@@ -108,7 +107,7 @@ export const handler = async (options: CheckoutOptions, logger?: Logger) => {
   if (options.clean) {
     await rimraf(workspace.workflowsPath);
   } else {
-    await tidyWorkflowDir(currentProject!, switchProject);
+    await tidyWorkflowDir(currentProject, switchProject, false, workspacePath);
   }
 
   // write the forked from map
diff --git a/packages/cli/src/projects/deploy.ts b/packages/cli/src/projects/deploy.ts
index 8549d481e..c355f2773 100644
--- a/packages/cli/src/projects/deploy.ts
+++ b/packages/cli/src/projects/deploy.ts
@@ -251,7 +251,7 @@ export async function handler(options: DeployOptions, logger: Logger) {
   // We need track alias in openfn.yaml to make this easier (and tracked in from fs)
   const ws = new Workspace(options.workspace || '.');
 
-  const active = ws.getActiveProject();
+  const active = ws.getTrackedProject();
   const alias = options.alias ?? active?.alias;
 
   const localProject = await Project.from('fs', {
diff --git a/packages/cli/src/projects/list.ts b/packages/cli/src/projects/list.ts
index dc1e84848..06d091c59 100644
--- a/packages/cli/src/projects/list.ts
+++ b/packages/cli/src/projects/list.ts
@@ -39,7 +39,7 @@ export const handler = async (options: ProjectListOptions, logger: Logger) => {
 
   logger.always(`Available openfn projects\n\n${workspace
     .list()
-    .map((p) => describeProject(p, p === workspace.getActiveProject()))
+    .map((p) => describeProject(p, p === workspace.getTrackedProject()))
     .join('\n\n')}
     `);
 };
diff --git a/packages/cli/src/projects/merge.ts b/packages/cli/src/projects/merge.ts
index 6b471e39a..7c9837c7d 100644
--- a/packages/cli/src/projects/merge.ts
+++ b/packages/cli/src/projects/merge.ts
@@ -71,7 +71,7 @@ export const handler = async (options: MergeOptions, logger: Logger) => {
     logger.debug('Loading target project from path', basePath);
     targetProject = await Project.from('path', basePath);
   } else {
-    targetProject = workspace.getActiveProject()!;
+    targetProject = workspace.getTrackedProject()!;
     if (!targetProject) {
       logger.error(`No project currently checked out`);
       return;
diff --git a/packages/cli/src/projects/util.ts b/packages/cli/src/projects/util.ts
index 43f847add..7a9185585 100644
--- a/packages/cli/src/projects/util.ts
+++ b/packages/cli/src/projects/util.ts
@@ -1,4 +1,5 @@
 import path from 'node:path';
+import fs from 'node:fs';
 import { mkdir, writeFile } from 'node:fs/promises';
 import { Provisioner } from '@openfn/lexicon/lightning';
 import { fetch } from 'undici';
@@ -214,7 +215,8 @@ class DeployError extends Error {
 export async function tidyWorkflowDir(
   currentProject: Project | undefined,
   incomingProject: Project | undefined,
-  dryRun = false
+  dryRun = false,
+  dirPath = '.'
 ) {
   if (!currentProject || !incomingProject) {
     return [];
@@ -232,7 +234,15 @@ export async function tidyWorkflowDir(
   }
 
   if (!dryRun) {
-    await rimraf(toRemove);
+    const abs = (p: string) => path.join(dirPath, p);
+    await rimraf(toRemove.map(abs));
+
+    const dirs = new Set(toRemove.map((f) => path.dirname(f)));
+    for (const dir of Array.from(dirs)) {
+      try {
+        fs.rmdirSync(abs(dir)); // throws when not empty
+      } catch {}
+    }
   }
 
   // Return and sort for testing
diff --git a/packages/cli/src/projects/version.ts b/packages/cli/src/projects/version.ts
index dfe0c90bf..94b20a893 100644
--- a/packages/cli/src/projects/version.ts
+++ b/packages/cli/src/projects/version.ts
@@ -32,7 +32,7 @@ export const handler = async (options: VersionOptions, logger: Logger) => {
 
   const output = new Map<string, string>();
 
-  const activeProject = workspace.getActiveProject();
+  const activeProject = await workspace.getCheckedOutProject();
   if (options.workflow) {
     const workflow = activeProject?.getWorkflow(options.workflow);
     if (!workflow) {
diff --git a/packages/cli/src/util/load-plan.ts b/packages/cli/src/util/load-plan.ts
index 203a7acb9..67180457d 100644
--- a/packages/cli/src/util/load-plan.ts
+++ b/packages/cli/src/util/load-plan.ts
@@ -62,7 +62,7 @@ const loadPlan = async (
     };
 
     options.credentials ??= workspace.getConfig().credentials;
-    options.collectionsEndpoint ??= proj.openfn?.endpoint;
+    options.collectionsEndpoint ??= proj?.openfn?.endpoint;
     // Set the cache path to be relative to the workflow
     options.cachePath ??= workspace.workflowsPath + `/${name}/${CACHE_DIR}`;
   }
diff --git a/packages/cli/test/projects/checkout.test.ts b/packages/cli/test/projects/checkout.test.ts
index 8f7f74add..2208de789 100644
--- a/packages/cli/test/projects/checkout.test.ts
+++ b/packages/cli/test/projects/checkout.test.ts
@@ -499,3 +499,127 @@ workspace:
     ],
   });
 });
+
+test.serial(
+  'checkout: removes old workflow directory when workflow is renamed on server',
+  async (t) => {
+    mock({
+      '/ws3/workflows/old-workflow': {
+        'old-workflow.yaml': jsonToYaml({
+          id: 'old-workflow',
+          steps: [{ id: 'run-job', expression: './run-job.js' }],
+        }),
+        'run-job.js': 'fn(state => state)',
+      },
+      '/ws3/openfn.yaml': jsonToYaml({ project: { id: 'main-project' } }),
+      '/ws3/.projects/main-project@server.yaml': jsonToYaml({
+        id: '<uuid:main>',
+        name: 'Main Project',
+        workflows: [
+          {
+            name: 'New Workflow',
+            jobs: [{ name: 'Run Job', body: 'fn(s => s)' }],
+            triggers: [],
+            edges: [],
+          },
+        ],
+      }),
+    });
+
+    await checkoutHandler(
+      {
+        command: 'project-checkout',
+        project: 'main-project',
+        workspace: '/ws3',
+      },
+      logger
+    );
+
+    t.false(fs.existsSync('/ws3/workflows/old-workflow'));
+    t.true(fs.existsSync('/ws3/workflows/new-workflow'));
+  }
+);
+
+test.serial(
+  'checkout: removes old step file when step is renamed on server',
+  async (t) => {
+    mock({
+      '/ws4/workflows/my-workflow': {
+        'my-workflow.yaml': jsonToYaml({
+          id: 'my-workflow',
+          steps: [{ id: 'old-step', expression: './old-step.js' }],
+        }),
+        'old-step.js': 'fn(state => state)',
+      },
+      '/ws4/openfn.yaml': jsonToYaml({ project: { id: 'main-project' } }),
+      '/ws4/.projects/main-project@server.yaml': jsonToYaml({
+        id: '<uuid:main>',
+        name: 'Main Project',
+        workflows: [
+          {
+            name: 'My Workflow',
+            jobs: [{ name: 'New Step', body: 'fn(s => s)' }],
+            triggers: [],
+            edges: [],
+          },
+      ],
+      }),
+    });
+
+    await checkoutHandler(
+      {
+        command: 'project-checkout',
+        project: 'main-project',
+        workspace: '/ws4',
+      },
+      logger
+    );
+
+    t.false(fs.existsSync('/ws4/workflows/my-workflow/old-step.js'));
+    t.true(fs.existsSync('/ws4/workflows/my-workflow/new-step.js'));
+    t.true(fs.existsSync('/ws4/workflows/my-workflow'));
+  }
+);
+
+test.serial(
+  'checkout: removes workflow directory when workflow is deleted on server',
+  async (t) => {
+    mock({
+      '/ws5/workflows/workflow-a': {
+        'workflow-a.yaml': jsonToYaml({
+          id: 'workflow-a',
+          steps: [{ id: 'run-job', expression: './run-job.js' }],
+        }),
+        'run-job.js': 'fn(state => state)',
+      },
+      '/ws5/workflows/workflow-b': {
+        'workflow-b.yaml': jsonToYaml({ id: 'workflow-b', steps: [] }),
+      },
+      '/ws5/openfn.yaml': jsonToYaml({ project: { id: 'main-project' } }),
+      '/ws5/.projects/main-project@server.yaml': jsonToYaml({
+        id: '<uuid:main>',
+        name: 'Main Project',
+        workflows: [
+          {
+            name: 'Workflow A',
+            jobs: [{ name: 'Run Job', body: 'fn(s => s)' }],
+            triggers: [],
+            edges: [],
+          },
+        ],
+      }),
+    });
+
+    await checkoutHandler(
+      {
+        command: 'project-checkout',
+        project: 'main-project',
+        workspace: '/ws5',
+      },
+      logger
+    );
+
+    t.false(fs.existsSync('/ws5/workflows/workflow-b'));
+    t.true(fs.existsSync('/ws5/workflows/workflow-a'));
+  }
+);
diff --git a/packages/project/src/Workspace.ts b/packages/project/src/Workspace.ts
index 618bdbcf2..0f7eb847b 100644
--- a/packages/project/src/Workspace.ts
+++ b/packages/project/src/Workspace.ts
@@ -116,15 +116,21 @@ export class Workspace {
     return this.projectPaths.get(id);
   }
 
-  getActiveProject() {
+  getTrackedProject() {
     return (
       this.projects.find((p) => p.openfn?.uuid === this.activeProject?.uuid) ??
       this.projects.find((p) => p.id === this.activeProject?.id)
     );
   }
 
-  getCheckedOutProject() {
-    return Project.from('fs', { root: this.root, config: this.config });
+  async getCheckedOutProject() {
+    return await Project.from('fs', {
+      root: this.root,
+      config: this.config,
+    }).catch((e) => {
+      if (e.code === 'ENOENT') return undefined;
+      throw e;
+    });
   }
 
   getCredentialMap() {