Hello,
First of all, I highly suggest making your post more friendly. More people will have the same issue, and they will be met with "How the hell do you use ...!?!?!?!??!?"
You can work around this issue without much effort. Look in the Transfers window in the target's File Explorer. Using FTP, manually copy all of these .elf files from the source path to the destination path. Transfering files directly within this program doesn't work properly in my case, and I assume you have the same issue.
I'm new to this as well, and haven't gotten much further than this (can't see anything in the Processes list).