Datapoint:
When I upgraded a flight well before the migration, it took the correct 2 credits.
After the migration, this appeared on my eUpgrade page:
This flight is now showing 4 credits taken (info included name, route and new PNR #)
Then this appears right below it. "Agent" manually adds back 2 credits.
The total credits available did not change, but the math of what was deducted for the flight did. No idea if this means new mileage charts are coming or if it was a blip caused by the migration.