We gave this a go this morning and it worked.
Step 1: Delete App Group ID from the old account.
Step 2: Recreate the Group ID in the new account.
Step 3: Let Xcode do it's thing and regenerate entitlements/profiles etc
After we did this all of our App Group functionality started to work. Data that was stored in our NSUserDefaults suite became available again.
On a side note it wasn't immediately clear to us that this would be an issue when we initiated the transfer. May I suggest adding App Group considerations to the documentation here: https://developer.apple.com/help/app-store-connect/transfer-an-app/overview-of-app-transfer