I reported this dec 2015 to Steinberg(yes, 2015) - but they wasted the ticket out in nowhere. Just does not exist - even though I have initial confirmation with title header etc. I have haunted Steinberg with this the last month - have to look up what happend - this will decide my future with Steinberg alltogether. I put many hours troubleshooting this and provided successful track archive and failed one. This is no way to treat customers.
I had that when saving to archive from a arbitrary track number in a project - I got that stuff, outputs all mixed up in order and also the dialog asking to delete tracks. So here I used maybe track 13, 18 and 25 or similar - and it becomes a mess when trying to load later. I did a folder with midi track and SD2 instrument track with 7 stereo outs and a bus.
Workaround was to redo saving to archive from a blank project, so SD2 and 7 outs and a bus for those were the only ones in that project.
That seemed to work.
If to do with tracks consequtive or not, don’t know.
So if disabled has the same problem as not starting at track 1 or something similar.