[eluser]Ben Edmunds[/eluser]
Deadly,
I recently did a migration of a user system to Ion Auth and the same general rules apply to your case.
The most important things to look out for is:
1. Using the same identity (email, username, etc)
2. Making sure the new system uses the same password encryption algorithm
This is of course if you want the change to be invisible to users so they can still login with their old credentials.