I have a very simple WiX project (version 3.7) that installs somes files (a .NET program version 6.0.0.0). I\'m ready to release a new version 6.0.1.0 using the MajorUpgrade
I have had the same problem. The issue here is when doing major upgrade, msi at first checks which components to install (and all dlls with lower version than the ones already installed are marked as "do not install"), then it removes installed app and then installs new version but without those previously marked components.
Rescheduling of REP did not help since "disallowing installation (...)" was done in Costing phase and MajorUpgrade can only be scheduled in Install phase.
My solution was to set REINSTALLMODE property to "amus" in wxs file.
The "a" means all dlls will be reinstalled despite their versions.