If a sync marker does not lie on a measure boundary, deleting all the measures from the measure containing the sync marker to the end of the tab will erase the marker. The same applies for the start and the end markers. Example:
Afterwards, the orange sync marker cannot be recovered by adding or deleting measures. However, it will show up again if new measures are created automatically at the end of the tab from note / chord insertions - more precisely, the deletion moves the sync marker to one measure past the end of the tab (measure 3 in this case), so YouTube sync will still somehow work even with the markers invisible.