progress.txt doesn't control what gets uploaded, that's filelist.txt.
Do you have .log.bz2 and .val.bz2 files, or just the .val.bz2 files? If you don't have any .log.bz2 files, then you don't have any actual data to upload. The .val.bz2 files are just extra residue more than anything else -- you can shut down the DF process and delete the .val.bz2 files. Unless, of course, there's a matching .log.bz2 file, then you don't want to delete the .val version.
If you do have pairs of files, and they aren't listed in filelist.txt, Ars' site, I believe, has a way to upload them.