The Join tool is an extremely useful, but somewhat neglected, part of Meshmixer. However if you can master Join you will be able to perform mesh repairs that otherwise would be very difficult.
The Erase/Fill tool is limited to filling "disc-shaped" holes, ie holes defined by a single boundary loop. The Join tool is used to fill "cylinder-shaped" holes, where you have two separate boundary loops and you wish to connect them with a cylinder-shaped tube. This is similar to the Tube Handle tool, except that you do not have the initial selections (because those areas are holes).
To use Join, you must select the rings of triangles around the two separate boundary loops. The boundry-loop-double-click shortcut in the Select tool will make this very easy. The join surface is automatically remeshed and smoothed to provide approximate tangent continuity.
Currently there are no modifiable properties for the Join tool. The shortcut key for the join tool is j.
The image above shows an example usage of Join. You can see that the surface does not pass through the initial boundary loops, shown in blue. This is because both input selections are deleted, so it is actually the neighbouring rings of triangles that are joined. The reason for this is that often the boundary loops in scan meshes contain the worst triangles in the mesh. Trying to enforce tangent continuity with these triangles would produce undesirable results. If your Join looks lumpy, or the join fails, try expanding the selections a few loops using the < > keys, and then run an optimize-selection pass with the o hotkey. You will often find the results are much better.
Below are a few more examples of Join, to give you a sense of just how powerful this tool is. Note, though, that in some spatial configurations it will fail to produce manifold output. One such example is shown in the bottom-right image. Although the holes are closed, the "line" where the surfaces join is a non-manifold edge.