My guess is that you'd better just recreate the appstack after office patches have been installed. Might be a lot of work but it should work then..
So the issue ended up being that we have two different Windows 10 builds in testing. One is LTSC and one is a main branch (1709). Most applications have no issues being captured on a 1709 provisioning box, but for whatever reason Visio/Project would have an issue if mounted to the opposite OS (and cause it to re-configure a few [but not all] of the office applications at initial load). I now have two different provisioning machines one for LTSC and one for CB (or whatever mainline build we would be running) to capture one or the other depending on use case.