Can you paint a box turtle's shell without hurting it?

Assuming you're talking about marking the shell in case it gets lost. The safest thing to do - would be to have the tortoise micro-chipped. That way, if it does get lost, it's simply a case of the finder taking the reptile to a vet - or calling animal control. Both of those organisations have scanners able to read the microchip - and will be able to contact the legitimate owner.