I have the same issue as described here: 
http://stackoverflow.com/questions/15138731/wix-major-upgrade-not-installing-all-files
After a major upgrade a few files are missing. After a repair, they 
reapper, and with a clean install, they are also correctly installed.
The log contains
Disallowing installation of component: {GUID-OF-COMPONENT} since the same 
component with higher versioned keyfile exists

The remove is currently scheduled as afterInstallInitialize.

To make sure that all files are really updated, I use this pattern for 
each file:
            <Component Directory="APPLICATIONFOLDER" Permanent="no" Guid="
c88f271e-6225-47a0-b3d7-a2ed7e8b3603" Id="
CotEm3PsKG0Qw7tmSelwF4HoqeWDPAs_IPcvyLhIKa94">
                <File Id="file1DGrKlnB0IDTi2JXC4XTtVRF3c.Y0zf2f8M9I9hdGpk" 
Source="#source#" />
                <RemoveFile Id='
removeFile1DGrKlnB0IDTi2JXC4XTtVRF3c.Y0zf2f8M9I9hdGpk' On='install' Name='
#name#'/>
            </Component>
Basically I want to just write all files contained in the MSI to disk, 
overwriting all existing files.
Guids and IDs are generated by System.Guid.NewGuid(), so the component 
rules are totally violated and I can't just change the scheduling of 
removeExisting.

What are my options to solve the issue?
I know I could use a stable ID/Guid generation algorithm (I could probably 
just use the one provided by Wix) so that the component rules are no 
longer violated and schedule it afterInstallExecute (or Finalize), but I 
would like to keep the current sequence where it is first uninstalled and 
then cleanly reinstalled.

Thank you,
Lukas
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