So, you mention "app stack" and other applications. Were these app stacks that came over from 2.x or were they captured natively on a modern version of app volumes?
Generally speaking, with app volumes 4, it's better to capture individual applications rather than having these large app stacks.
Have you tested with updating your app volumes agent? It would seem to me that the issue is some user state data that must be getting captured by fslogix. Have you tried disabling fslogix on a test image post upgrade?