I recreated the .MSI file today, and reran the installation with the
following command:
msiexec /i
C:\Installs\WixWindowsService2012Setup\bin\Release\WixWindowsService2012Setup.msi
/l*v C:\Installs\WixWindowsService2012Setup\bin\Release\install.log.

It still overrides the config file, and this is from the log file:

MSI (s) (00:9C) [09:59:20:624]: Executing op:
FileRemove(,FileName=WixWindowsService2012.exe.config,,ComponentId={blabla})
MSI (s) (00:9C) [09:59:20:626]: Verifying accessibility of file:
WixWindowsService2012.exe.config

MSI (s) (00:64) [09:59:20:715]: Executing op:
ComponentRegister(ComponentId={blabla},KeyPath=C:\Program
Files\WixWindowsService2012\WixWindowsService2012.exe.config,State=3,,Disk=1,SharedDllRefCount=0,BinaryType=1)

MSI (s) (00:64) [09:59:21:042]: Executing op:
FileCopy(SourceName=fctymilg.con|WixWindowsService2012.exe.config,SourceCabKey=WixWindowsService2012.exe.config,DestName=WixWindowsService2012.exe.config,Attributes=512,FileSize=538,PerTick=65536,,VerifyMedia=1,,,,,CheckCRC=0,,,InstallMode=58982400,HashOptions=0,HashPart1=1770114632,HashPart2=-1876651659,HashPart3=212308780,HashPart4=-2030918298,,)

MSI (s) (00:64) [09:59:21:043]: File: C:\Program
Files\WixWindowsService2012\WixWindowsService2012.exe.config;   To be
installed;      Won't patch;    No existing file
MSI (s) (00:64) [09:59:21:043]: Source for file
'WixWindowsService2012.exe.config' is compressed

Why does the installation remove and copy the file, even though the config
file in the installer has a different date and time with the config file on
the installed folder ?

Thank you.




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