It won't ruin them, however I would suggest doing it a little differently than some of the videos that are around. Do you have broiler pot or a steamer insert? It's best to not let them sit directly on the bottom of the pot, if you do be prepared to lose about 15-20% of them.
Before you boil them.......
Do this, place them in a bowl of water for an hour or so (hot/cold it doesn't matter), then rubber band them together and run some hot water
through them from the sink. The rubber band will keep them from falling all over the place under the hot water and allow the drain out.
This will rid them of the bulk of any residual
juice, remove the rubber band and boil them. Then, blow them all out (or stick the bastor in the mouthpiece end and use it to blow them out) then set them out as you said, and they'll be fine.