A bugged beekeeper stands around somewhere with the job "install colony in hive"; i.e. _stands_, doing absolutely nothing while displaying an active job. In that case, you have to find the empty hive that issued the installation job and toggle its install option off and on. Finding the building can be done by consulting the "j"obs list, zooming to the "b"uilding, or by looking at i"t"ems in buildings, singling out hives which contain no bees.
Are you sure the hives in question are actually ready for harvesting? The indicator in the building dialogue says "ready to split", which is a different thing - a new colony can be split off and placed in an empty hive. This happens quite a while before harvesting becomes possible. A hive is ready to harvest when there are a "royal jelly" and a "honeycomb" item inside the building. To see those, you have to check the i"t"ems contained in the hives. Once hives are ready to harvest and at least one unoccupied dwarf with beekeeping enabled is available, "collect hive products" should show up soon enough.
@^Disabling beekeeping or otherwise yanking the beekeeper around will not fix the stuckness bug. The faulty job comes from the hive, and the hive alone. As long as you don't fix the building, the job will not clear up and will keep stranding beekeepers.