As Scott says (and I'm trying to say!) it's okay to keep thinned or mixed paints seperately from the base colors. Just don't contaminate your good paint with the mixed though, it will either congeal as Eric pointed out, or will wreck the base colour.
I have read that you shouldn't even keep thinned paints at all, but I can't figure out why not? I kept some mixed green zinc chromate and the bottle didn't seal properly and the thinner evaporated leaving a smooth glossy bit of plastic behind (I use acrylics), so that might be why. I now put a small square of plastic food wrap on the bottle before screwing the top back on. That not only seems to help with leaks, but I haven't struggled with a stuck lid since.