I have to replace it because of a bug that blocks the software uninstallation, but Windows can't find the MSI file if I use the file search utility, but I think the MSI is stored somewhere where the Add or Remove Programs utility can use it.
Does it not go into %windir%\installer\?
Though I think that the files may get renamed. Not sure where you get the name mapping from...
This directory gets very big so I move it to an external drive. This sometimes cause uninstalls or updates to fail with a missing msi error, but this can be fixed by putting the directory back.