Habmin is not showing the mesh, as in routes. It is just showing the neighbors the devices have reported to the controller. The network topology displayed in Habmin is not showing routes, so nodes may look disconnected but they can still communicate. A network heal is only available in the development version of the zwave binding, which is likely to be merged into master (the nightly snapshots) soon.
Zensys Tools is available from Axial Control (http://docs.incontrolha.com/home/remove-a-failed-device). A newer(?) version that looks to have limited fumctionality is also distributed with Aeon Labs firmware updates. There is only a Windows binary and I have not been successful running it under Wine (they did something odd with com port discovery).