I tested 9.5.41 - and as far as I can see - problem remains.
A short recapture of how it become for me
#1. this works as workaround - making a small Project template, with the instrument and a bus on adjacent tracks.
Like for superiordrummer2 on instrument track, 7 stereo out on track 1 and a bus for it on track 2.
Select those two tracks and export selected tracks(to archive).
This can be restored sucessfully - before in Cubase 8 up to now.
Order of everything is as saved - in mixer with outs and project windows with automation.
#2. This is a failing example - from an existing project superiordrummer 7 outs on instrument track is on track 29, and bus on track 33.
Select those two tracks and export selected tracks(to archive).
This become mockup when restored. Outs in mixer are scrambled order of outs, and same on automation lanes in project windows.
Out 2 and 3, snare and hihat in my case, end up last instead of first.
Two extra automation lanes as well are created - become not track color(red in my case for instruments) but gray.
These two gray extra something can be marked and removed, so not sure what cubase these are - some kind of inputs or something.
If this propblem is what I think it is - this order of outs become mocked up and have to do with order of original tracks save - I think problem with disbaled tracks remain as well. I guess some kind of loosing track of order of things that belong together when something is lost in between.
I have similar result when making a BlueCatAudio Patchwork loaded with four midi vst plugins of piz, and two samplers for a brass section.
Workaround with making special project where those to be saved - are adjacent to each other - makes all the difference.
So not taking random project and just save random tracks from it to archive - and try to restore later - I have a workaround since Cubase 8.x.
So preparing special project when what you save with tracks adjacent to each other - it seems to make a difference.
Now you can place group channels(busses) anywhere and less of a problem to make a workaround, but worse if to take from a project where busses are placed in separate folder - then track order will be far apart and think problem bigger.
So I say this is not working as intended yet.