Two cases: if the Captain realizes why the FO has called STOP he may reply CONTINUE or GO.
If he doesn't realize the reason, he better listen to the FO, who, don't forget, can also exercise his emergency authority.
FO are not monkeys, and sometimes much brighter than the Captain!
At the end of the fair, there will never be an absolute truth, as usual, and people capable of improvising, with good common sense, have got some more chanches to get it right, IMHO.