Apparently this has happened before so maybe, for this specific issue, a cron job could check the Packages.gz file and recreate it (flush the cache) if it didn't pass the test (gunzip, verify contents etc)...

EDIT -> Maybe the current import job should just check if the import went well before replacing the index (Packages.gz). I'm guessing it doesn't...

Interesting reading: http://mirrorer.alioth.debian.org/reprepro.1.html