Interestingly, automatic identification of previously unidentified albums didn’t cause the “clean-up”. I will keep an eye on it when the next batch of albums gets identified tomorrow. If the custom genre sticks then most is fine. If I do a forced / manual identification, it’s not much trouble to reassign a genre.
Update: Indeed genre(s) assigned manually did stick while Roon did an automatic identification in the background again.
Summary: So it’s just when an identification is forced manually only genres from file tags are kept if set so in preferences but not genres (created and) assigned inside the Roon application.
Since I do know this now and nobody else seems to have a problem with it I mark it as (self) solved.