Angels have the Phone Box
If you told it to save all apps and settings, it should have done that. There are 2 separate boxes that need to be checked.
I have upgraded 3 computers so far, 2 using the GWX upgrade method, and 1 using the media creation tool to create an ISO. All three of them upgraded with applications and settings in place. I can't imagine why your apps would be missing if you checked the box to keep them. I have not heard of anyone else having this problem. Sorry I can't be of more help.