After i beat chapter 3 i would like to change kira and scourge's saber color. Havent got up to shadow of revan and the expansions yet but will the cutscenes reflect the saber color changes or will they revert back to green and red respectively?

They be whatever colour you want to change it to in cutscenes etc.

 

Lana is the only character (I think) who will always have her red crystal in cut scenes.

I don't know if this has changed, but I thought all the Kotfe characters have fixed lightsaber appearances. I once tried to give Senya a purple Lightsaber crystal and she still appeared in her duel with Vaylin with a blue lightsaber. In fact, her hilt in the cutscene was different than the one she carries in gameplay.

 

Kira and Scourge have sabers that are changeable though. I distinctly remember giving Kira a blue Double Saber for the mission to take down Angral on the Desolator.