How can I stop Windows Installer "repairing" my application?

I have an application that installs SQL scripts with it. After running the SQL scripts, I want them to be deleted (along with other aspects of the installation) so users cannot work out the structure of the database.

However, after deleting them and running the application, Windows Installer comes up with the message

"Please wait while Windows Installer configures (my app)"

After the message, all the files I deleted are reinstated. How can I prevent Windows Installer reinstating these files?
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This autorepair is most likely triggered by an advertised shortcut, if you replace the current shortcut of the application by one which is made by hand (pointing to the executable) it should stop triggering the autoreapair.
theskintmanAuthor Commented:
I'm triggering this just running the executable from its directory, not using a shortcut at all - it's just Windows Installer interrupting at the point the application is executed.
Ok other option is removing the keyfiles to the files you want to have removed, but that requires some knowledge (more then I have) of MSIs
This is what I know of it,
Keyfiles (at least I think the called that way) are checkpoints which are checked if an application is started an repaired if they are missing or currupt.
When you  use an MSI editor (like installshield admin studio) you can remove the keyfile property from the files you don't want to trigger a repair.

Make sure you have a backup of the original MSI, and remove the installation completely before installing the adjusted MSI.

Just to make clear.
My knowledge of MSI's is limited, so I'm not sure if this works ! and I have no way to test this at my current location.

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Try this one may help u
Download Windows installer cleanup..;en-us;290301

Install the application
Run the application (From start>Programs>Windows installer cleanup)
Select All & clean all ..
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