Thanks for clarifying. Unfortunately, in the situation as you describe it, there's no easy programmatic way to determine which you have loaded. If you haven't modified the variables, you could load each of the MAT files into a structure:
then compare the values of your workspace variables to those in the structure and see which file matches.
If you're willing to do it interactively, you could just go back through your Command History, and see which file was loaded. Even if you double-click a file, the load command will be run in the Command Window, so it should show in your history.
If you're looking to make a workflow around this, though, you could ease the pain with a little planning. I'd suggest making a separate script you can call to save a workspace. In that function, check if "filename" already exists in the workspace. If so, use it to save the file. If not, select a new filename to save to and save that variable with the filename in it. That way, any variables you load from MAT files in the future will already tell you where they came from and where to save to.
-Cam
