I tend to believe the evil points remain.
The evil points are associated with an IP. The ban is associated with a profile UID.

For example if a new account is created and receives a proxyban by default that user can be whitelisted/unbanned, but the evil points are not erased. If he/she were to create another user I am pretty sure that one would be proxybanned as well.

So yeah... pretty sure unbanning does not reduce the evil point score.