cgsecurity.org

I have a 2TB WD Passport external hard drive and I'm sure it's partially corrupted.

I've used TestDisk to copy over about 80% of the files that were on my hard drive, but two folders in particular appear to be empty. I know those files are "there" since I can sometimes access them when I (slowly) browse the hard drive through Windows Explorer, but I of course can't copy/move them over.

Are these files lost and do I just use PhotoRec to try and salvage whatever I can?

You should clone the disk to a new empty one using ddrescue as described in https://www.cgsecurity.org/testdisk.pdf
Once it's done, remove the original disk and try to copy your files from the clone.
It should work better. If it's not the case, you can always use PhotoRec on the clone.