Firstbase-a somewhat open-ended question, which likely requires the removal of the windows, and an inspection and opinion from a professional shipright to answer definitively. Issues like the moisture level, the extent of moisture intrusion, what core material, how deep are your pockets, what's your standard of repair, etc. all influence going forward.
In VERY general terms, moisture plus organic material (wood in cores, for instance) equals rot. Simply "plugging the leaks" won't mitigate the moisture issue already in the core. In time, the core will fail. Again, in general terms, drying of the core prior to sealing the leaks is best. There are some treatments that claim miracle cures for displacing and sealing wet wood. Depending on all the findings in para no. 1, they might be appropriate. The only sure cure for an abnormal level of moisture in cores is to expose it, dry it, reef out and repair any damage, and go from there.
"Helping" the core dry out is a tough issue, depending on where the boat's located. Water molecules travel from wet to dry (no surprise there!), so enclosing the affected area in a relatively dryer environment to promote that transport is paramount. Heat helps also. Vacuum bagging might help too. Simply rebedding the windows without mitigating the moisture is, IMHO, a waste of time and $$$. Ditto application of goo like Smith's Epoxy or Git-Rot.
I'm sure that last statement will unleash a volley of objection from the proponents of fast-fixes by application of a variety of snake oils to core materials in order to mitigate water absorption! Do what works best for you in your circumstance. All the best in your endeavor.
Regards,
Pete