Yes, it will change. Your Pikachu's thunderbolt base power will be decreased down to 90
Moves power are changed in XY, so the Pokemon from previous gens that has a move that has been changed, that move will be changed. The programming of XY was to lower selected moves, such as thunderbolt. Since the game has no data for a 95 base power thunderbolt, it will only have the data for a 90 base power thunderbolt, so Therefore, it will change.
Hope I helped, sorry for the misconvience.
Source: Experience with Japanese pokebank Pokemon, knowledge