Bern's transition to the Reformation

The Fribourgeois and Bernese formed an alliance to conquer parts of the Pays de Vaud in 1475. But with Bern's transition to the Reformation and Fribourg's decision to remain faithful to the old faith, things became complicated. Which side would the joint bailiwicks of Orbe, Echallens and Grandson fall on? How should this religious mix be organized on a day-to-day basis?