The subject of wet coring comes up a lot in
http://www.plasticclassicforum.com/ . Do a search there and you will find numerous threads on the subject. I suggest paying particular attention to comments made by "Tim". the forum administrator and a professional fiberglass boat renovator.
It's usually more cost effective to cut off one of the skins over (or under) the affected area, remove the soaked and rotten core, clean, abate and bond in a new core, then bond the old skin back down. A lot less patching to do and the work can be done very quickly.
In a nutshell that is by far the best way. Anything else is just a quick fix and prone to failure, if it even does anything at all. Moisture trapped in the core will virtually never dry out. And even if it did, you will never rebond the core to the skins effectively.
"Nothing is more permanent than a temporary fix".