Ive been in this position before, but in my car. Was night time, traffic was chocka and a car was indicating to turn across the lane, so I flashed to let him in. Being a cyclist I always check mirrors before doing this to make sure that there is no one filtering on my left (which IMHO is a no-no anyway, but people still do it) and it proved clear.
Just as the other driver was about to complete his maneuver, Ninja cyclist appears at my wing mirror. Luckily the mrs had her window open so I managed to shout stop to him, which he fortunately did.
Then questioned the lack of lights and his filtering position; he was oblivious to breaking the law without any lights on as I had just proven and didnt seem to understand my concern at his safety.
So my point is this: I am sure, that if you drive, there will be times when you flash someone without checking for cyclists. Ive only been cycling for a year now, and in the above situation, before cycling I dare say that I wouldn't have checked my mirrors for cyclists.
My 2p worth.