I hate to send you off to another forum, but you might want to check to see if breezesystems has their own forum just for their products. You might get an answer faster that way.
I'm not sure I understand your problem though. Maybe your way of working is different than mine. This is how I work with zoombrowser and I don't think it would change with Downloader Pro.
1) I have a CF card with some pictures on it, so I put it into my card reader.
2) I run zoombrowser and tell it to download the files. I tell it to copy them into a directory based in /pictures/pictures originals, and to create a directory in there based on the date the picture was taken. I then select only new files and tell it to start copying..
3) When its done copying, I startup Photoshop and start looking at the pictures. If I edit one, I create a directory in /pictures/pictures edited that has the date the picture was taken for the name. I save the edited copy into that directory.
It sounds like you are mixing step 2 with step 3. Why are you want to use Downloader Pro to "download" files that you edited? It's for downloading pictures that are on a portable flash media card (SD, CF, Memory Stick,...) Once the files are off the media card, youn're done using the downloading software (zoombrowser's downloader or Downloader Pro.) Can you describe what you are trying to do in a way similar to how I describe it above? I think I'm missing something here.