I think you mean the window with the option to disable user settings. Yes I am aware of this.
I don’t always get this. But it is likely that after a crash on loading as described, it will then show this message the next time I try to load. As I say it is not consistent.
Vienna usually crashes too and the VSL crash report almost always points at a Synchron instance (either Synchron player or Synchron piano, not always the same) but after long dialogs with their support and report sharing, this appears to be a red herring.
Cubase prefs is ALWAYS the key to getting it going again.
Cubase does not always create a report. I don’t know the criteria it sets - but reading other posts on this forum it suggests that Cubase has to be actually running first before a crash will produce a report. I guess I can see why that might be…
I have to say that this does seem to bear out my own experience. As I say it is not completely constistent.
I have four crash reports from Cubase since 9th Sept (about a week ago) - but in actual fact Cubase has crashed on load more like 15 or 20 times in that timeframe. More perhaps.
The last Cubase crash report (from earlier today) indicates a problem with Voxengo MSED VST (ie: not the VST3 version) - but I’m pretty convinced that’s not the REAL problem. I have removed it from the system though just in case.
Going back to my original post - what I am trying to find out here is where Cubase saves its Mackie midi setup data - so that I can continue to work with some workarounds.
Obviously it would be lovely to get to the bottom of the problem - but I’m hoping (as usually occurs) that eventually a new update of software (not just Cubase, but other stuff too) will make the fault redundant… and then there will probably be a whole new set of issues!! 
It was interesting (not the adjective I used at the time, I had a few choicer ones to hand) that updating Mac OS made absolutely no difference at all to the symptoms!! I honestly thought it it would… Even the system drive had been re-formatted.
I must also point out to go with that that these projects I’m having trouble with… many of them are many months old and older, and had previously behaved faultlessly, so it’s not a corrupt project type issue. And the projects are all on a separate SSD