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k 4 PC can be buggy - though Amazon won't admit it., especially after a few local software version updates.
the quickest way to test whether you've lost your cloud data would be to fresh install K for PC on a different PC and attempt to download your notes, collections etc from cloud. IF they arrive corrupted than your cloud data is messed up. if they arrive OK on the new PC, then it's your local data on the other PC that is corrupted, and maybe a total registry clean, delete app data folders etc will be needed.
Getting the books themselves into Calibre is trivial, the extra disc space for 5000 books is not great, but I don't think calibre can do anythiing about the book related notes. they live in separate little files, I per book & I think add-books leaves them behind ( I could be wrong about that)
calibre has powerful tools for creating new collections but some human input of logic & time will be needed
add books also wrongly populates first name, last name author fields from Kindle books, which is an extra annoyance
somewhere on the amazon site is a techie Kindle forum & you could cross post there for more advice
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