Yes, it will delete all ebooks that are automatically added. That is so it doesn't add the same file millions of times. If you just use K4PC to download new books, that shouldn't be a problem.
calibre will not automatically add from your kindle unless you chose your kindle as the folder to be automatically added.
DRM messages should still add the book, just the book will be DRM'ed are you SURE the book isn't there despite the message?
DRM is a separate issue, and if your books are DRM'ed then having them in calibre will pretty much do you nothing anyway, My advice is (if you haven't already) to google apprentice alf.
And installing older versions of calibre will not help you do things calibre was never meant, designed, or given the capability to do.
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