Its ok to fill them, but you have to cut open the top of the fiberglass stringers. clean out all the wood before filling.
I am thinking when you get to good wood you will have to glass over it before you fill so the filler has something to stick to, as it will not stick to wood.
Good luck and take lots of pic's!!
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1986 V20 
Old Fishermen never die, we just SMELL that way!!
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