Hi Geert, sorry for takign so much time.
Yes we were in correct dialog.
The issue was, that one MDG was "as a part of the model" and another MDG was "imported from user".
The 2 MDGs were exactly the same, except one was outdated. Somehow EA library (of our MDG) decided to use the outdated version which caused consistency issues with the rest of our documents.
Anyhow, we fixed it by exporting XML, deleting the MDG of the user under %app, opening the latest "okay" version in our versioning system and imported XML again.
No work was lost.
Thanks for support!