I have a buffer with antifoam in it, but over time what I believe to be is silicone is forming globules. Filtering works but I lose antifoam functionality. Is there a way to remove these globules while retaining antifoam functionality
Silicone anti-foaming agents work well. See: https://en.wikipedia.org/wiki/Defoamer
Your only routes are to change the type (see the wiki entry) or (try to) reduce the quantity of the silicone used. Remove the silicone completely and the anti-foaming properties will be lost.