Unchanged file during MajorUpdate leads to file missing after reboot

[mo22]

I have the following test setup:

dotnet tool install --global wix
wix --version
5.0.2+aa65968c

And this test WXS file:

<Wix xmlns="http://wixtoolset.org/schemas/v4/wxs">
  <Package Name="MyApp" Language="1033" Manufacturer="Me" Version="$(var.Version)" UpgradeCode="77f0a2cc-9731-48d0-b704-1f76b2eea4ef" InstallerVersion="405">
    <MajorUpgrade DowngradeErrorMessage="A newer version of [ProductName] is already installed." AllowSameVersionUpgrades="yes" />
    <!-- separate .cab files, otherwise .msi file gets too large -->
    <MediaTemplate EmbedCab="no" />
    <ComponentGroupRef Id="Files" />
  </Package>
  <Fragment>
    <StandardDirectory Id="ProgramFiles64Folder">
      <Directory Id="INSTALLFOLDER" Name="MyApp">
      </Directory>
    </StandardDirectory>
    <ComponentGroup Id="Files" Directory="INSTALLFOLDER">
      <Files Include=".\dist\**" />
    </ComponentGroup>
  </Fragment>
</Wix>

In the dist directory are the files to be installed in the program files folder, among them is my.exe

Now I'm updating an existing installation, and in that update the file my.exe is unchanged, the following does show up in the msiexec log file:

MSI (s) (68:38) [16:36:23:834]: Verifying accessibility of file: my.exe
MSI (s) (68:38) [16:36:23:834]: Note: 1: 2205 2:  3: Error
MSI (s) (68:38) [16:36:23:834]: Note: 1: 2228 2:  3: Error 4: SELECT `Message` FROM `Error` WHERE `Error` = 1903
Info 1903.Scheduling reboot operation: Deleting file C:\Program Files\MyApp\my.exe. Must reboot to complete operation.
[...]
MSI (s) (68:78) [16:36:59:695]: Executing op: FileCopy(SourceName=my.exe,SourceCabKey=flsKtzzZ3VXb.pLLKiHl7g6HJe2i7k,DestName=scriba.exe,Attributes=512,FileSize=330248,PerTick=65536,,VerifyMedia=1,,,,,CheckCRC=0,,,InstallMode=58982400,HashOptions=0,HashPart1=1646957652,HashPart2=-1441641143,HashPart3=-631674000,HashPart4=239543849,,)
MSI (s) (68:78) [16:36:59:695]: File: C:\Program Files\MyApp\my.exe;    Won't Overwrite;    Won't patch;    Existing file is unversioned and unmodified - hash matches source file

I understand that MSI wants to:

• uninstall the previous product
• fails to remove the file my.exe as it is in use
• instead schedules the removal after reboot (fine until here)
• wants to write the new my.exe
• finds that the still-in-use existing my.exe hash matches

After then rebooting the my.exe is gone.

The same appears with other files.

Any hints on how to resolve this, other than making the install folder version dependent?

Thank you very much

Moritz