The shield is only in place till they achieve FTL, it wont be there at the start of the sequel. It is apart of Faust preserving the humans and other AIF races. The humans will also have intelligence and strength boosts courtesy of Faust.

Also the reborn Equestrians will be unaware of both the supremes and Triarians. They will lack any knowledge of the previous Equestrian empire or anything regarding the universal war and prior to that. Tbe reborn Equestrians will actually stick to peace so the supremes looking down on them is sorta stupid as they have no association with the Equestrians that the supremes knew