I'm still using my Freepages site, but given the changes there over the years I'm aware that it could close down some time. I have a separate website, mainly a kind of photo album, and when looking at possible hosts for it I've always tried to make sure it could also accommodate the site from Freepages should that ever become necessary.
From what you write, it sounds as though you don't have a local copy of your Freepages site, which is different from the way I've worked. I've always worked on the site on my PC and kept my files and back-ups locally, then just uploaded pages as and when they've changed.
I used to do this with FireFTP, a Firefox plug-in, but as that doesn't work with the latest version of Firefox I've switched to a standalone FTP program - there are a few free options available. I think this would help with your problem too - once logged in you get an explorer-type view of the site, so you can locate and download files from wherever they may be lurking.