You should be OK with 3000 books. There have been a few people here claiming to have 5000 or more books with no real problems. Personally, I think the maximum I have had is about 2000. The Glo HD is at about 1800 at the moment with no problems.
Do you have an idea of when the corruption happens? At eject time, or are you seeing a hang or crash? Are you putting all 3000 books on the device and letting them process? Or building up to it in smaller batches?
Batches of a few hundred would be what I would try. Between batches you can connect and backup the database. That will let you recover if the next batch has problems.
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