After working with a model (installing or deleting it), issuing the Set-AxModel -NoInstallMode has no effect, meaning that you still get the ModelStore has changed window, and even selecting Skip in the UI, this happens again when you reopen the AX client.
If this happens, chances are that the issue comes not from a model still being marked as Dirty in the modelstore database, but rather it's an issue with your upgrade (or update) checklists.
My fix for this issue was simple, because the error just appeared our of the blue, in the middle of just doing some model management tasks, and to get things moving without spending too much, I called in a T-Sql statement: so just opened SSMS and ran:
set MinorUpgrade = 0
How I got to this statement: debug and observing (recalling) the Info -> Startup method's code: that is the place where the checklists are being started from., if needed (a lot of good items to look at, will cover them in a separate topic).
However, when writing this post, I actually realized that I did install on that instance a new CU (9),so from here the resulting setup of this (in my example however, no data or code upgrade was necessary, so the fix worked just fine; in your case, you'll have to decide).