You can copy the WU into 2 different folders and run them that way. The first one uploaded will get credit. The other will be considered a duplicate and you'll get an error. You can actually just run that 2nd one with a -stop_after_process (I think that's the switch) or it might be that you put a blank file in the directory called stop_after_process.txt and "touch" it (once the processing is done, it'll see that file, will stop, and will not try to upload).
Also, if you run X, I'd highly recommend getting KSetiwatch. I don't have the link handy but I think a link is available from Seti's Unix add-on page. Cool program that'll let you monitor your WU progress on all your *nix machines (it utilizes NFS). The other way is to keep checking the state.sah file and estimate how long it'll take. However, from what I've heard about the betas, it might be a bit tricky to try to estimate the times with this new client.