I would be more inclined to add drainage trenches around the outside of run,
hopefully you have a bit of slope and some lower ground nearby.
I still think that 'deep' litter' (mostly wood chippings) would be better than sand.
When you had flooding, was there standing water inside the coop/run?
I'm not sure, would be pretty hard to lay a barrier that would keep the sand from sifting down into the current bedding as the chickens scratch, it would have to be solid not mesh....and they may scratch it up eventually.
So if you really want sand in there I would remove all the current...
Is your coop 'floor' dirt?
Do you also have a run?
Does it flood from the bad drainage?
Sand + chicken poop(you can never sift all the poop out) + dampness = stinky.
I would not use mesh or screening on any floor/ground where chickens walk/scratch/dig.
Pics of the area might help.