All the "solar" cover really does (at least the normal blue inexpensive ones) is retain heat in the pool by retarding evaporation. Evaporation can cause HUGE heat loss from the pool, and yes, it does happen when the air is cold. Wind and dry air will suck heat from the pool big time.

So, I would concur that cutting the cover shouldn't be a killer, as long as that doesn't wind up allowing the wind to shift the cover and expose too much pool surface.