Strange upgrade issue

[Steve0212a]

I have a WIX v4.05 bundle that has an MSI and some prerequisites in it. For this, I am only talking about the WIX MSI. I do a dotnet publish and publish to a folder with our compiled code. I then use HarvestDirectory in the WIX MSI WixProj to build an MSI.

My issue is that sometimes after the upgrade, it is missing files. Clean installs have no issue - it is only on upgrades. Further, it is not on all upgrades, but only happens sometimes. In my last test, it was missing System.Data.SqlClient.dll. The following lines from the log contain either the component id or the file name.

MSI (s) (E4:D4) [10:18:57:411]: Disallowing installation of component: {437EC653-4B3E-52F0-95A5-0277BD4F4DF6} since the same component with higher versioned keyfile exists
.
.
MSI (s) (E4:AC) [10:20:07:829]: Executing op: UnregisterSharedComponentProvider(Component={437EC653-4B3E-52F0-95A5-0277BD4F4DF6},ProductCode={1123FEF6-7DED-4FBA-B1DD-0AE13BD16E62})
MSI (s) (E4:AC) [10:20:07:829]: Executing op: ComponentUnregister(ComponentId={437EC653-4B3E-52F0-95A5-0277BD4F4DF6},,BinaryType=1,)
.
.
MSI (s) (E4:AC) [10:20:21:452]: Executing op: FileRemove(,FileName=System.Data.SqlClient.dll,,ComponentId={437EC653-4B3E-52F0-95A5-0277BD4F4DF6})
MSI (s) (E4:AC) [10:20:21:454]: Verifying accessibility of file: System.Data.SqlClient.dll
.
.
MSI (s) (E4:D4) [10:21:38:442]: Executing op: ComponentRegister(ComponentId={437EC653-4B3E-52F0-95A5-0277BD4F4DF6},KeyPath=<redacted path>\System.Data.SqlClient.dll,State=3,,Disk=1,SharedDllRefCount=0,BinaryType=1)

My guess is that what is happening is that it thinks it should not install the file ("Disallowing installation of component"), but then still removes the old file. I did some googling and came across https://stackoverflow.com/a/35524424/336681 which says to move "RemoveExistingProducts" before costing. I tried adding this to my InstallExecuteSequence:

<RemoveExistingProducts Before="CostInitialize" />

but got this error message. I tried setting overridable, but then it was overridden and didn't fix my issue.

error WIX0170: The InstallExecuteSequence table contains an action 'RemoveExistingProducts' that is declared in two different locations. Please remove one of the actions or set the Overridable='yes' attribute on one of their elements.

That compile error led me to this discussion: https://github.com/orgs/wixtoolset/discussions/8100 which says it won't be fixed until WIX v6.

I also thought this would fix it (already had that in our WXS), but it did not and still said the component would be disallowed.

<Property Id="REINSTALLMODE" Value="amus" />

Sorry for the long winded explanation. Is there any way that I can do an upgrade and tell it to overwrite files even if they are older or to move the remove before costing (assuming that would fix it)?

thanks

[Steve0212a]

I was out on vacation last week. Is there anyone that has any ideas how I can fix this?