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fix: Reject deleted flags and segments in flag overrides #1080

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Run time

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Job	Run time
sdist (functional)	3m 32s
linux (3.11)	11m 32s
windows (3.12)	9m 13s
linux (3.10)	11m 39s
linux (3.12)	12m 4s
linux (3.13)	11m 52s
linux (3.14)	11m 51s
windows (3.14)	9m 44s
windows (3.13)	9m 5s
windows (3.11)	9m 18s
windows (3.10)	8m 33s
	1h 48m 23s