I think the issue where disabling/re-enabling MIDI tracks doesn’t re-connect to the correct instrument track destination is known, but I’ve been noticing a spinoff bug of this.
If I disable/enable a track and it breaks the connections, I can fix everything (all tracks playing properly), save the project, load the project and unrelated tracks now have broken MIDI → instrument connections.
Just wanted to report that this is an additional side-effect of that particularly frustrating bug.