Are you talking about the brass "cap nut" as indicated by the white arrow in the pic below? If so, it just holds the linkage together (under spring pressure), so once installed it has nothing more to do with the carb sync procedure.
Take it off, clear all the debris out of the threads and try to reinstall it as squarely as possible. As long as it tightens up adequately against the spring, it'll be fine. The sync is done with the screws indentfied by the green arrows.