As long as nobody is changing from krkr2 to krkrz the saves should be fully compatible. It would be relatively easy to actually just have the installer move any file with the extension *.xp3 out of faterealtanua_savedata and move it into a backup folder.
As for Fate.exe I did some poking through .rsrc and the defaults for the following debug-type settings are as follows: debug=no, forcelog=no, logerror=yes, movie_reg_rot=no
That being said they can be overridden at anytime by specifying otherwise when launching via command line. (movie_reg_rot allows you to use GraphEdit in the DirectX SDK to debug movie related issues.)
Unfortunately it looks like an actual debugging tool isn't going to fly. My knowledge of c++ isn't yet good enough. Going to have to trace function calls the hard way. (Just now realizing the logs do that too. Why the hell was I bothering with it again. Should have listened to Quibi when he said it's a waste of time)
PS: Most of what I say regarding any issue is nothing more than speculation because if I can find the issue I can fix the issue. And if I can fix the issue than I wouldn't be speculating anymore lol.