You tested deleting them one by one out of transaction. Did you test a
version without ancestor relations set too? (Just these relations may
be the reason, as change is blocked within an ancestor group as long
as another change is not finished.)

If such tests don't help, maybe it's an appengine issue. In your place
I would create some demo code and upload it to a test page with two
buttons (create 10 items, delete 5 items) always showing the resulting
number, thus demonstrating that deleting sometimes failes.

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