I'm completely new to flood and drain growing.

My seedlings are ready to transport into my flood and drain system. My only concern is? The jiffy pellets that i start the seedlings in are really nice and are doing really good so far. But my only concern is the over all results during the actual on-going process.
I can't help but wonder if the seedlings or pellets rather will eventually dissipate in the flood and drain system. Can anyone will more experience help me with this question?!

THANKS!!!