Hey Thomas,
If I understand you correctly, you want to update a database that was changed in version 1.0.0.2, from your new update 1.0.0.3. The script or exe you're executing in the temporary folder will run no matter the version you're updating from. This means you need to add some logic to your script. You can do this a few different ways, but by far the best solution to your problem is to version your database schemas. That is, store the schema version in a table, then modify your update script to bail out if the schema version is the latest (e.g. "... WHERE schema_version = '1.0.0.2' ..." ).