Supposing the Pokemon is already transferred to gen 6, then yes. Same as transferring from gen 5 to gen 6, once transferred, it remains in that generation, and its moveset will change accordingly. This is part of the reason you cannot transfer Pokemon backwards in generations, with the exception of gen 2's Time Capsule. If you want to teach a Pokemon in gen 1 a gen 6 learned move, it would fail, as it would be using its learnset from gen 1. Long story short, whenever you move a Pokemon into a different generation, the Pokemon's moveset reflects that generation.
Source: Experience and Reasoning
