Well the schism happened in 1054. EU4 starts in 1444 and the reformation happens in the early 16th century. Point is, Christianity had changed so much by that point that mending the schism likely wouldn't have had much effect. You can also look at the Council of Ferrara-Florence in 1439 (which led to the Laetentur Caeli, the papal bull), just before the EU4 start date. Emperor John VIII Palaiologos sought reconciliation with the western church as a means to provide diplomatic opportunities to get protection from the Turks. The treaty was signed and everything seemed good, but after the council the eastern bishops found that the general population and local authorities did not accept the unification, so the schism remained.
All of this is to say that mending the schism in EU4 through means of conquest probably wouldn't have had too much effect on the catholic and protestant nations. It might even aggravate the catholics, and the pope would just relocate to some other part of Europe (like the Avignon papacy in the 14th century). Or they would follow the in-game event where papacy is disabled and everyone is just ok with it. Maybe just a single event triggered by the restoration of the pentarchy that gives all catholic nations the choice to convert to orthodoxy. AI would be 80% weighted to remain Catholic. Staying Catholic gives a malus opinion with orthodox nations and maybe a small hit to prestige or something. Converting to Orthodoxy would give a few years of national unrest, but also boosted missionary strength (like protestant nations when they convert) and a temporary boost to relations with orthodox nations.
Basically I don't think mending the schism would have too serious of an effect in the era of EU4.
