I think I finally got it all back to normal.
I did as explained here and went all the way with "Open in save mode, click away all the error messages, open the project, erase the plugin and save again".
That basically works.
In between that idea of a possible shortcut with just erasing the plugins from the plugin folder caused some extra trouble. And when I put it back from the trash and rescanned the plugin folder that didn't work right away either.
It is just a lot of popups and clicking and sometimes you overlook a popup because it is behind the preference window and then opening the project too early causes another crash and so on and on...
 
Thanks for all your help.
 
But why (and this is the one question I would still like to ask) did these plugins work in X3 and not in Professional?
That can be really irritating because retrospectively examining where and how you used those plugins is much worse than having plugins that don't work at all right from the start.
Well, it probably falls into the category of "things happen, don't make changes without fallback option, etc. ;-)