+1 but you can actually do this via workaround if you simply create a copy of the BIAB app in the same folder.
then you can launch two instances of the same app and ( i think... ) cut and paste between them.
Nochai, You are correct that you can have multiple instances of BiaB open at a time. You don't even have to make a copy of the BiaB app. However, you do have to make a change in the program preferences. Press Ctrl + E or select Options > Preferences to open the preferences window then enable the "Allow multiple instances of Band-in-a-Box to be running" selection.
But, you are not able to copy and paste between instances.