Does SapphireIMS figure out machines which are missing agent vs actual available machines in organization using some reconciliation method?

Yes, SapphireIMS supports inventory reconcile specifically for missing agents by comparing all hostnames/IP address of agents rolled out versus sources like CMDB computer list, Active directory computer list or through computer list populated using CSV file. This helps to know whether we have inventory of all the machines.

You can configure and view the list of machines which are missing agent using help link –