[wix-users] IIS App Pool Settings not retained during Major Upgrade

[Ven H]

I have the following App Pool element in my wxs file.

<iis:WebAppPool Id="MyDefaultPool" Name="My Default Pool"
ManagedPipelineMode="Classic" IdleTimeout="0" MaxWorkerProcesses="1"
ManagedRuntimeVersion="v4.0"  PrivateMemory="1800000" />

This creates the app pool as expected when the MSI is installed. After
that, I manually modify some settings like IdleTimeout to 5 minutes and
ManagedRuntimeVersion to v2.0.

I have a MajorUpgrade element with Schedule="afterInstallExecute". After I
run a major upgrade with the same wxs file with the same settings for web
app pool as given above, my manual changes get replaced. Is there a way to
retain the manually made changes? Please help.