Python CI

Fix: use new snapshot id in deleted manifest entry unless is existing… #5970

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Run time

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Job	Run time
lint-and-test (3.11)	4m 25s
lint-and-test (3.9)	5m 10s
lint-and-test (3.12)	4m 17s
integration-test (3.9)	12m 56s
integration-test (3.10)	12m 15s
integration-test (3.11)	13m 11s
lint-and-test (3.10)	4m 15s
integration-test (3.12)	12m 34s
	1h 9m 3s