So I ported a save from a version pre-GOG and even though the game lets me access my save files and finish missions, the mission select screen still says I need to finish the federation campaign. I'm already finished with Assimilation on the borg side. But it kicks me back to mission select with only the first federation mission available.

Is there any way for me to access the other missions without starting all over?

Also I have tried going back to an old save and using the kobayashimaru cheat, it kicks me back to the main menu same as before.

EDIT: What does seem to work is starting with the first mission, and then using the cheat to skip. Tedius, but it works.