Ok, in addition to my two previous questions:
I just did the workflow that thomasb suggested.
I opened a new project with the mal-aligned images and a few more correct ones of the area.
I aligned them (took 40000/80000 to work) and then exported the registration.
This I imported as a component into the big project but nothing changed.
Am I missing something?
Do I have to rerun alignment?
Which would loop back to one of my original questions:
Wouldn’t that result in a competely new alignment?
Or is the new one based on the previous alignments?
Help! 