My actual Calibre folder is fine, by library I meant the libraries in justread. I currently have 3 justread libraries: Default (where the duplicate files are located), Test (where I switched to initially for doing tests), FF (the new one I made after messing up my Default folder).
Now, if I change my justread library to Test then go back to FF, all books are New when I check in Calibre Sync. I didn't make any changes to these books prior to switching justread libraries. These are the same books as I left them in Calibre the software and FF the justread library. Although when I sync these New books to FF they now overwrite the same books in FF, I don't know why they were duplicates in my old Default library. That solves that problem at least.
EDIT: I guess my question is, why does switching libraries make justread "lose memory" of sync data when you switch back to that library?
Also, I imagine the Covers folder in justread will keep getting populated with book covers since the user only manually deletes an old library folder. Easy enough to delete the covers anyway.