If you make separate tilesets, there will be NO performance impact. If you try to do it via script, there WILL be a performance impact, because you're asking it to do extra processing. If you do it the tileset way, you are not relying on anyone but yourself. If you use a script, you're relying on someone to give you the script or to write it for you. I know which one I'd be doing.
Just make extra copies of the tile sheets, edit them to make them black and white, and save them. Duplicate the tileset in the Tilesets tab and then substitute the b/w tile sheets in each of the slots. Then you can either make copies of your maps, or use the Change Tileset command. I'd probably make copies of the map to remove unused events (assuming your flashbacks are all cutscenes and the player doesn't get to actually play on them) and just have those necessary for the cutscene.
Sepia is often preferred for flashback scenes, I believe - more of a nostalgic look than black and white.