I think you are right - the disabled track issue is worse than track archive in general.
Even more sad it wasn’t taken care of then - it would fix both parts like track archive too.
In the root - it’s the same issue - keeping track of what belongs together and how.
And you get the same symtom slike scrambled order of output and extra automation lanes Cubase does not know what it is.
You don’t want to continue working on a project showing those symptoms - you never know what turns up later when everything is added and saved and stuff.
But I think it’s a good hint - that saving what arbitrary tracks or track neighbours makes a difference in track archive thingy.
Hope you get it sorted - even in 9.5.50 - but I’m leaving Steinberg now, I’m done.