Looks like this is caused by adding a vanilla "Viewport" viewlayer and making it the first in the list
(special case in do_version_layers_to_collections() if there are layer overrides...)

Render Layers node stores an index to viewlayers afaics and by just making a new viewlayer the first here is shifting all others by one...
Not sure why the new vanilla "Viewport" viewlayer needs to be the first in the list?
If that needs to be the case, then Render Layers nodes indices need to be corrected as well, I guess.
But just removing the "push-to-head" for the new vanilla viewlayer also solves this issue

I can't see a reason why it must be first in the list.