Hello o.w.matter and welcome to the forum
Which version of the game are you playing, Enderal FS (Classic) or the Enderal Special Edition?
Have you ever used console commands before?
Basically, be careful with it. Some (such as setstage) can cause permanent errors that also write themselves into the savegame.
Please send us a suitable savegame. Then we are able to see if we can reproduce the problem.
Preferably a recent one and one before the completion of Part 1.
You can find them for the Classic version under: C:\Users\...\Documents\my games\Enderal\Saves
or for the Special Edition under: C:\Users\...\Documents\my games\Enderal Special Edition\Saves
We'll need the *.ess and the *.skse file.
Best a manual save (no auto or quicksave).
Pack both to a zip or rar archive (the forum software doesn't accept *.skse format).