Thanks Jacob, I am a “new user of the month” so I had enough rights to send Angelo a PM with my personal information 
I can confirm the modified version of DynamoCore (2.1.1.8720) solved the issue. Several times following the steps as before and the script opens without any issue. As a test I did it again with the old DLL and the issue appears again.
@angelohbwang: I am curious what is the difference, what did you change?
Also how can I be sure there are no other issues? You can’t either of course 
Is it an idea to be more descriptive if Dynamo can’t read nodes? Instead of leaving them out, a warning messagebox to not save the file, or adding dummy nodes? I’d put on the console view, else I would have missed every message about missing nodes.
@Michael_Kirschner2: I was planning to set up a dummy app with the same behavior as our company app but since it is solved in the new Core, I won’t spend time doing this. Maybe Angelo can explain what he did (so we have a clue what caused the issue).
Anyway, thank you all very much for all your efforts to improve the software!