This treatment has to be done on solid medium? Otherwise you could use liquid medium and recover seeds through sedimentation/filtration.

For recovering a bunch of Arabidopsis seedlings from solid medium with minimum damage I plated the seeds on cellophane circles fitting the Petri dish. Water, salts and other supplements can go through the paper allowing normal growth of the seedlings compared to normal growth conditions (just roots grow on the surface). That could also work for your seeds, they can be easily collected from the cellophane surface. For sterilization of cellophane circles place them intercalated with filter paper, otherwise they will stick to each other.

Dialysis tubing could also be an option, I guess...

Thanks so much