Hello Chris,
If where it was is now flush, I'd imagine that you would beed to pull the tailshaft out, slide the yoke completely out and then tap it out. By tap I do not mean knock, rather the same process used to remove a bolt shank having sheared the head off.
Bits of metal will otherwise end up inside and these will need to be removed completely. You could take the tailshaft complete to a driveline specialist and allow them to remove and install a new nipple if you wished.
Ron.