Guy Senneville replies: I would guess that if you were using an oil base stain there could potentially be a problem. If you were using a dye there is no problem. The safest bet is to protect before stain if you are not sure. Something as simple as masking tape should do the trick.
Marty Milkovits replies: If you are using an oil based stain, definitely protect the edges. And even with a water based stain you will be comprising the integrity of the joint although nowhere near as much as with a oil stain.