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I'm sorry I can't answer your question. I hope someone else does.
But I would like to ask: Why do you find it necessary to store 5,000 books in your Kindle for PC application? Do you plan to actually read all those books in the near future? Are these books that you have already read and perhaps want to refer to again?
It seems to me it would be so much easier to keep the relevant files in a directory on your computer - with or without using Calibre to organise them into collections - and to copy a file to the Kindle directory when you want to read the book. Once you have finished reading it, just delete it from the Kindle directory. That way, you have a way of keeping track of the books, you won't have duplicates of 5,000 files, and the whole thing will be much easier to manage.
If I am missing something obvious, my apologies. In any case, I hope you find a solution to your original problem.
Mike
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