@gdaydigger-
Are you trying to add several hundred books at one time? Bad idea. As ixtab already suggested, add the books in small increments and wait for them to index. When you get to a group that doesn't finish indexing, it is likely that the 'broken' book is within that group. Work through them one at a time until you find the problem book file. By the way, you may well have more than one 'broken' file. The books that are already on your Kindle and have fully indexed are probably fine...look at the ones not showing up.
After running into this problem myself, I never add more than 10-20 books at a time and always wait for them to finish indexing and appear on my Kindle before adding more.
I am not aware of any short-cut to this process. Good luck!
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