Do you mean that U need to replace glass where the shrouds penetrate the deck, or where the chainplate attaches to the hull, via wooden knees, etc.? This is a crucial area of structural support for the rigging. If it is rotted, then U may want to seek some professioanl advice on how to fix it. A bad / inappropriate fix will do more harm then good. But on the other hand, I've seen more boat owners be much more consientious about there repairs then boat yards are.
Can U be more specific about where there is damage?