Wow, you were quick. Sorry, coming a bit late now I guess, but this issue of soft cores is just a tad exaggerated. (ask me how I know) If the soft spots are only here and there, and you can stop up any leaks and stop further water entry, then ripping up the top fibreglass layer and replacing all the coring, is perhaps in some cases overkill. If no more water gets in, then the threat of it the damp working its way into the cabin walls is probably very unlikely, and to do the whole shebang is very expensive. Remember, the damp core is still sandwiched between two layers of fibreglass, so even if there are holes drilled in the top layer, it is unlikely the lower layer has been pierced, so the damp is not going anywhere as long as no more water gets in.
A more limited removal of core, (or even leaving it, as the PO of my boat did, with no issues 16 years later), then repairing that layer (seeing you have already ripped up the teak), with the option then of another layer of fibreglass non-skid over the top of it all - or - glueing down faux teak as suggested by Gerryhebear above, which in itself will stiffen the deck up again, is also an option, albeit more expensive. And that faux teak will get hot underfoot in summer, make no mistake about that.
