I would suggest reaming out the core and isolating it with thickened epoxy. The fact that no damage has occurred yet doesn't mean it won't. It is just a hole at this point and, as you rebed everything, are you really willing to risk MORE core damage after your extensive rebuild?
Remember, the core damage you've found thus far was due, in large part, to fairly shoddy construction technique. There's no good reason to make the same mistake and doing it right will only add a day to the project.
