If you back up the .bak & .dat files (you'll need to back up both, save them in a safe place) in your incomplete folder, you should be able to copy them into the new incomplete folder (when you revert back to the old version)... that should let your incomplete downloads resume from where they left off.
I haven't had to do this myself but from what I've read... if you lose the .dat & .bak files then your download will have to start from 0% again