I just spent over 30 hours backing up a soon-to-be-removed website. Upon
finishing, I went back to check my files and noticed one or two pages were
missing. I started to download them, and in the process all the pages I had
recently downloaded were no longer where they used to be.

Where are they? I really can't wrap my mind around the idea that all the files
would delete themselves just to update a small part - and that this would mean
I'd have to tie my computer up for another day and a half to do nothing.