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Start by making a backup of the calibre library, that way you can keep trying different things.
The easiest could be to do as you suggest, create a new empty calibre library and add the books from the old, assuming they are there and there are opf-files with metadata in the folders.
Move or rename the calibre library. Then start calibre. A new empty library will be created.
Add the books in the old calibre library. Choose the second method, add books in subdirectories, assume that multiple books in the same folder is the same book in different formats.
After a while you have hopefully a new working and up to date calibre library.
When you experiment with networked and mirrored folders it is a good idea to make sure you have a backup, if something goes wrong. It is NOT recommended to use networked folders for the calibre library, bad things can happen. Test carefully, and make sure not to update or mirror the calibre library while you have calibre running.
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