You didn't say, but what alerted you that it was an underfill? How frustrating (to put it really mildly)!!! I'd talk to the endo on the phone or in person before doing the onlay; a good endo isn't going to knowingly create a problem. Mine actually said to me, "I'd hate to have you put a crown on this and then have to come back in a year." I know it's aggrevating and frustrating and tiring, but fix it now if you are going to. Will you be worried about it if you don't go back for a re-treat? If so, I'd cancel with the prosthodontist, unfortunately.
Think of it as a mental health issue as well as a dental one...didn't mean to rhyme there.