WIX Toolset 220.127.116.116
The Difxapp extension is incompatible with delta patching due to a sequencing error. When a delta patch is created the resulting InstallExecuteSequence table has MsiProcessDrivers@4001 and PatchFiles@4090. As a result the existing driver is reinstalled and the new driver is never installed.
Since the sequencing of neither action is overridable there is currently no work around I can find.
Sample project to reproduce the issue: DifxSample.zip
We would have to see if we can resequence the custom action.