Best just to start with the clean, empty library of your current Calibre install. Use a find duplicates program like Singlemizer to remove the dupes from the old library folder, unless you're 100% certain it's all duplicates - if so just delete the old library folder. Probably wise to double-check the new library folder is an empty folder as well.
The only way I can see that it would import every doc on the computer is if you did a bulk import with add books and told it to start scanning at the computer's root folder. Just don't do that again.. Check out the videos tutorials in the main forum sticky:
https://www.mobileread.com/forums/sho...d.php?t=118596