Make a backup of the directory.
Then do a search for messages describing what to do with a missing filelist.txt file. (I remember others being told to look for filelist.tmp? ) If you're lucky, you should be able to upload most of the generations in the directory from the backup file; by renaming it filelist.txt (although you want to keep the current filelist.txt file to upload the rest of the files.)
You might want to download the november 20th foldtrajlite.exe file to get rid of the "can't set coordinates" errors.
And on Monday, Elena will hopefully give you directions on uploading the whole directory to them, in case it's something they want to look at.
Anyone have links to the discussions on tracking down the missing filelist tmp files?
Good luck..