DO NOT USE R-D-20 or any similar quaternary ammonium disinfectant on protocorms. Intact external tissues of mature plants are quite resisitant to this type of product, but protocorms are not much more than naked cells. No thick protective layers. Most actual fungicides should be reasonably safe though. Some can be used in plant tissue culture.

Protocorms can survive in situations like this, they certainly do in nature, but at this stage they would be reliant on symbiotic fungi for nutrients. Without a sterile environment it will be difficult to supply those nutrients without bacteria and fungi taking over. Good luck.