Also, should the DM want to have two encounters in a row where the ongoing effects fade, he need only interrupt that short rest somehow, then have the enounter a little more than 5 minutes later. For instance, if you're in hostile territory and snipers take pot shots at you every few minutes. There's no actual combat nless you can get to them before they disappear, but it will still stop you from resting and replenishing your encounter powers.
I wouldn't recommend it unless the PCs are deep within the heart of an enemy encampment, and have hopefully gone into the situation knowing that rest might not be an option. I'd definitely combine the planned encounters together into a single XP pool, and pull a little out to make up for the fact that they won't have "scene long" effects for the "entire scene."