App pools disappearing on upgrade
I have a very large server installer. It has over 11,000 files. There are several web sites and 5 new app pools. I am doing a major upgrade. For some reason on this upgrade, 2 of the app pools get removed and don’t get re-added.
I tried just about everything, changing upgrade settings, associating the app pools with another component, changing guids and deleting the app pools and re-adding them. I also created another installer with the same app pools and it installs them fine.
The installer takes about an hour to build once and run, so trying stuff takes a while.
On a clean install it works fine.

Any ideas?