[Sabardeyn]

I'm not sure I've understood your second post, but I believe there is confusion about the term "Library". Here is what I believe to be the issue...

Well, if your Complete Library hasn't been brought into calibre, then the software cannot directly affect it's contents. Calibre has to have a specific file structure for it's ebook libraries and uses the records in the database (metadata.db file in the library's parent folder) to make sure the files and file structure are as expected and to alter things as needed when the ebook's metadata is edited in calibre.

So calibre cannot manage what it effectively doesn't know about. Because your "Complete Library" is not a Library - not in the calibre sense. Your "Complete Library" is a manual collection of ebook files.

So you would need to create a new Library within calibre (anywhere on your computer system). Add all of the books from your "Complete Library" into this new Library (just copying files over will not work). Once that is done, and everything in this new Library is all set, you could copy it's parent folder - and all of it's contents - to your flash drive.

You would also need to delete and then re-add that newly created Library from the Library Icon's listing (Quick Switch, etc) to reset the path for the Switch Library function. (Because once you copy the new Library to it's new home, calibre's going to still be looking at it's old location.)

At this point, if you didn't want an extra copy, you could delete the original "Complete Library" content as it is no longer needed.