Dave...your decision probably hinges mostly on how good your fit was when you bought your flatbar bike. If the bike is a hint too big, having a longer top tube than for a std. drop bar fit, will only accentuate the problem. Conversely, if you bought the flat bar bike true to size or toward the small side of range...then it is no big deal. It really comes down to how the bike feels to you with a drop bar...how good your fit is with a shorter stem.
None of us keep our frames forever anyway and some like to experiment with different frame geometries..sometimes often. No doubt you will change frames at some point as well if for no other reason than to experiment.
Have fun.