Maybe you could "turn off" the screen by writing solid black fix layer tiles on the screen (for one frame) to hide the sprite layer while you are updating the palettes?
Possibly the snow effect could be hidden with fix layer tiles too?

Or if your render method is fast enough you could maybe increase the resolution by displaying only the half of the screen lines per frame
(similar to interlaced video: https://de.wikipedia.org/wiki/Zeilensprungverfahren) but it could cause the screen flicker too much.