With a little luck, he didn't put all 1000 on them at once and can guess from the date the problems started which books may cause this. Then you can delete them, see if it makes a difference and if yes, put them back one by one until you can reproduce the issue.
The same can be done for all 1000 if you don't know. It's a lot of work, but it's probably better than having a non-functioning ebook-reader.
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