I strongly recommend you grind that area out and recover in epoxy and glass cloth.  It is apparently leaking and thus is only going to get worse.  When you remove the glass/epoxy, leave the area open for a few days with a heat lamp nearby (not close enough to set it on fire!).  You can get a meter that will read the moisture content and based on that will tell you when you can recover.  With water in the wood, coating it with epoxy will only make it worse.  It has to be dry with a substantially reduced moisture content.  Others here on the forum can tell you what that should be.  

hi steve, 

i have a lot of boats (almost 20) under my belt and, unfortunately, this happens sometimes....where sections of the epoxy, for some reason, never fully cures.  of course, this is exasperated during the summer months when the un-fully-cured-epoxy becomes softer and, as you described, is less noticable during cold months.

so i disagree with sinkworhty that this is in any way indicative of a 'water leak'.  a water leak is very distinctive and different than epoxy that does not fully cure.

as for repair,  the approach is relatively straight forward and i would break it down as follows:

• outline the 'soft epoxy section' by carefully probing with a dull nail.  if you can 'dent' the epoxy, it is not fully cured.  if you cannot easily dent it...its fine.  through probing you can define an outline of the area of 'not fully cured epoxy' and you can mark it off with a pen or pencil.
• use a razor knife to carefully cut into the skin around the outline of the uncured epoxy and use a spatula or chisel to remove the glass/epoxy that is not fully cured.  since it is not fully cured, you will find you can just sort of peel it off.  a heat gun can help in this process if it is a little more sticky than allows you to easily peel it away by hand.
• once you have the piece off, you can sand and or use a scraper to remove any of the reamining uncured epoxy.
• sand the area to clean up any residual uncured epoxy and to bevel the good glass into the repair area.  this is similar to the repair approach you would take if you snagged something and scratched through the epoxy/glass layer and were just doing a normal skin repair.  rub it down with some denatured alcohol to clean it up before applying the repair.
• lay in the new glass over the wood and the bevel edged of the good glass and epoxy with fresh epoxy.   wet it out, and apply fill coats as necessary.
• use a sanding block to clean up the edged of the repair and blend it into the old/good glass.   
• re-apply any varnish or paint as necessary.

for whatever its worth, you can do this repair during the off season and it does not typically require 'immediate' attention....you have survived with it like this now for over a year...or so it seems from your description.   if it was a water leak....you would see a very clear stain/discolloration and that should be attended to immediately.

also make sure the 'new' epoxy does not have the same problem as the orgiinal.   if i was not actually buying new epoxy, i would do a test batch to ensure that i can get the old stuff to actually cure.  there are a number of reasons that epoxy may not properly cure ranging from defective ingredients to an improper mix of ingredients that are just fine.  you just want to have some confidence that you are not repeating the mistake even though you may never fully know what happened that caused the problem in the first place.

i can appreciate how frustrating it is...and a search of the literature will show, that while not common, it happens.  so i feel for you.     but the repair is pretty straight forward and if done well, will never be noticed.

all the best, 

h