When you want to trap SHB or other pests. If your bees haven’t drawn much comb yet, that won’t be a problem, I would leave it in the upper position. If you do move it to the lower position, the idea is that now the bees can’t reach it (unless you have a faulty mesh in your SBB) and you can coat it with Vaseline, cooking spray or sprinkled insecticidal diatomaceous earth to trap and kill what falls on it.
When you harvest, it needs to be clean and free of anything noxious. You then put it back in the upper slot so that the bees can reach it again to lick off any spilled honey. That keeps robbers and ants away from the hive.
As Adam says, removing it will probably decrease ventilation, because bees are very good at generating a kind of laminar flow in the hive if they have a somewhat restricted entrance. If you take the board out, they can’t do that. Some people remove it hoping that varroa, moth larvae and SHB will fall out of the hive. I would prefer to use it as a trap and clean it off periodically. You even cut a new board very inexpensively. I made some spares from this:
http://www.amazon.com/Highway-Traffic-Supply-Coroplast-5-pack/dp/B00EQFOSCQ/ref=sr_1_3?ie=UTF8&qid=1463386327&sr=8-3&keywords=4mm+coroplast
If you are going to leave the board in, it doesn’t really matter whether they are over open air or not. If you are going to take it out completely, you probably want a way for debris to be able to fall to the ground.