The TopoFusion.ini file stores the filenames of every loaded file. So the easiest way would be to have two copies of it that you copy back and forth (perhaps a .bat file).
What would be nice is the concept of a "portfolio" file that could be opened to load different groups of files.
But yes, you can't have two versions of TopoFusion installed since you can only register one copy of GPSMaster.ocx. It is possible to run different versions by running:
regsvr32 "c:\program files\topofusion2\GPSMaster.ocx"
for the version/directory you want to run. But this is a bit of a pain, too.