It will still be possible, but it will be a little more complicated. The filelist.txt is always there now, even just after you have uploaded. Where before you could just copy all of the data files and the filelist.txt and then delete them, now you have to deal with the filelist.txt changing after the upload but still being around. Sample filelist.txt:
./fold_1_handle_26_handle_protein_25.log.bz2
./handle_1_handle_protein_25_0000027.val
fold_1_handle_48_handle_protein_26.log.bz2
handle_1_handle_protein_26_0000049.val
CurrentStruc 1 51 124 26 1 49 7.287 -1923.725 -118.015 -830.829 41623948.000 1.450 2.700 1337.566 ------------------------------------------------------------------------------------------------
91c45dc6795e6cd38262d53c2aa0b109
I think that to start with you would have to watch what happens on a system that is connected to the internet when you upload and see which files it leaves behind and what the filelist.txt looks like after the upload.
Actually, I just remembered something that will make it harder. You can't edit the filelist.txt because it uses a key to prevent that. So what you would have to do would be stop folding on the unconnected machine, copy all of the data files and the filelist.txt and move them to the upload machine. Upload the data and then move the filelist.txt file back to the unconnected machine and then delete all of the files that got uploaded.
I don't see any way of moving the files on to your drive and then just starting that machine back up, unless you started over on a new set.
I think in order for the new system to continue to be on the forefront of sneaker net distributed computing there would need to be a new function. Some way to upload the data into a folder and then leave the working folder in a state just like it uploaded to the server.
./foldtrajlite -n native -f protein -ut -x:../results
would put the upload part in the results folder and leave the working folder ready to go.