The Close Cracks tool solves a few irritating problems that arise in mesh-based modeling. One has to do with imported meshes that contain disconnected internal boundaries. In these cases you will see thin blue "crack" edges, where the crack actually has identical boundary loops on either side, but they are topologically separated (for example many OBJ files with texture seams are created this way). The Close Cracks tool will weld these cracks together, if possible. However it does not do any complex stitching, and if welding vertices would involve any non-trivial movement or create non-manifold geometry, the crack will not be closed.
Close Cracks is also incredibly useful if you would like to apply operations to a sub-region of a mesh. Meshmixer does not have masking functionality, and some tools can only be applied to entire mesh objects. So, if you would like to work on a sub-region, you can select that region, use Edit > Separate to isolate it, apply the operation, then Combine with the original object and Close Cracks. The only critical requirement is that the operations you apply not change the mesh boundary; otherwise, you will no longer have a clean "crack").
This is also good way to work on the "inside" of meshes, that you otherwise would not be able to see. It will also let you isolate sub-regions of meshes that are otherwise too large to work with due to slow rendering updates.
The images below show how to use this workflow to isolate a region for 3D sculpting. The ear is Separated, sculpted, and Combined, and then Close Cracks merges the meshes into a single continuous shell. Note that during the sculpting the Fixed Boundary filter must be checked to precisely preserve the boundary loop.
