Migration Wizard

I ran the migration wizard from a wimdows 2003 with EV 9.0.3 and ran the import onto a windows 2008 r2 with the same EV 9.0.3 version.

I was under the impression it would export all registry keys and reimport all the registry keys onto the new server but to my suprise some custom one's were not imported like SynchInMigrationMode it did not replicate to new server. Our configuration depends greathly on that key and perhaps other wihin the 8 years we have EV in production. 

Does any one have any idea why, I'm I to go through every entries from the old server and compare it within the new server.