Is it possible you close the client too early?
After a hand is FINISHED, within 5 seconds PokerStars will update the handhistory file.
When you play Zoom/Rush, wait for much, much longer (2 minutes!) before you close the client after a session, because the hands you quickfolded in a row, all still have to be played out before the handhistory file is updated.
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You can also email PokerStars support, request all your handhistories, then run a import from file on the file they email you.
Are you saying that even the file they email you is incomplete and is definitely missing hands?