Question about painting accessories in cars.

Ok so i was thinking , i want to paint my mudflaps the same colour as my car, but if i do, i would paint them and clear coat them, then later if i wanted to trim the mudflaps an inch or so from the bottom of the flap, i would cut them with shears but would that mess up the paintjob on them or not? and if it does then if i want to repaint, do i have to take off all the old paint or can i paint on top of a clearcoat? or what?

You would need to add a flex agent to the paint and the clear coat, or else it will crack.

Trimming the flap would mess up the paint. It would at least leave an unsealed edge which would allow the paint to start lifting at the cut. At worst, the paint would flake off as you cut. If this happens, just scuff sand the existing paint on the flap and respray a thin coat. If the accumulated paint is too thick it may crack instead of flexing.