This stuff will penetrate far beyond the bad wood and into the still good balsa, protecting it as well. It will also displace light moisture. Then give it about a week or week and a half to cure out. Polyurethane sealants will bond with CPES to give you the tightest seal. This way you are protecting the balsa and at the same time eliminating the source of water leakage into the deck core.
Boats are work.
If you have any more questions or better definition about the procedure, let me know. We'll help all we can.