Yes, it is legitimate to call it a (huge) bug, but I think it was done by design for performance reasons. If they disable teams that are not used, processing will speed up.
Of course, we now have this ugly side effect. I too, have rule files with cups that draw teams from e.g. an inactive lower division.
My workaround is to set the nr of teams for divisions that I didn't make rules for. That way the teams are not set to extinct.
In your case you could set the nr of teams for "Amateurliga" to a certain value.
It's a workaround! Not saying that it will be a happy solution for everyone. Of course I'd also prefer that all teams are untouched, and hopefully there will be a fix soon, but if it is done by design it may take a while before this gets reviewed and fixed at all.