combine large libraries

[nccoast]

Hi,

Originally, I set up calibre wrong (I see now, looking at directions and manuals, etc.) I had a large ebook directory, copied it to my PC, and when I first installed calibre, pointed it to that directory. It seemed to work fine- have been finding and downloading books to my kindle for years.
I just obtained another very large stash of books from a friend, and tried to add them properly, and it didn't work- I got 780 pages of errors, permission denied [Errno 13].

Can I uninstall calibre, copy the new books onto the old directory, re-install, and point it to that directory again, and let it make a new database? I don't touch it, except to add a few books now and then- don't have any customizations at all.
I also have the original copy of that big directory on an external drive, so I could delete everything and start again, if that makes better sense.
Thanks for any help anybody is willing to give.
Cheers