I’ve just tried a basic test on this, loading one instance of Kontakt 6 and an a single instrument from ProjectSAM’s Symphobia, then duplicating up to 128 instances. All seemed normal there - I enabled all outs and routed the 128th instance of Kontakt through a group, closed and re-opened and thus far everything seemed normal and snappy. (Win 10 Pro, 7820X).
Oggfish, can you repro starting from a blank project somehow?
The disabled tracks thing is another matter, and this is definitely buggy even on simple projects. Just routing a multi-out instrument track to a folder, disabling, closing the project and re-opening loses the routings. Its very similar to a 3 year old bug that only got fixed around a year ago, and its back like a bad penny. Steinberg are aware, and the issue is logged in the system.