well I'm having the same problem, even if I do install 9944 over modbranch_2021 it will just not open after I run the install. The exe just doesn't run.
To be completely honest, it’s a little hard to guess what could be going wrong with code that I wrote 5 years ago
I bet people on game’s Discord would have more ideas than me at this point.
I found a way
after installing 9944 over modbranch_2021 rename the original NT to something else, rename NTT to "nuclearthrone" and open it through steam
Prengus, your solution worked for me. Thank you.