If you don't mind loading all books one more time, then
- wipe your SD card (format in in Windows, for instance)
- On the reader, go to Settings > Advanced Settings > Format internal memory
Note: this will wipe your reader clean (duh, but it can't hurt to mention). For me this clears up any issues with collections etc.
Then try dropping the whole CD again, 100 books loaded in one go really shouldn't pose that much of a problem for the reader.
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