Project archiving

Quartus archiver should do it. Note that an archive/unarchive will make all the files a sub-directory of the project(you don't want the unarchiver putting files randomly all over a new location), so if that wasn't your original setup then it will look different.

When you add the files in the beginning, you can make them relative, which I recommend.

I'm surprised modifying the .qsf is that difficult. If they're all in one or two locations, a search and replace should do it. I would generally do that since you can see exactly what is done.