When using System Center Configuration Manager sometimes managed devices disappear from the Console. These devices may still be in use und therefore should not be deleted, but continue to be managed via SCCM. The disappearance is controlled by a concealed option within the Site Maintenance of SCCM.
The Site Maintenance Options in the SCCM Console can be found at Administration -> Site Configuration -> Sites. Right click on the Site and select “Site Maintenance”.
Here are several Maintenance Tasks that can be activated and will start actions in defined periods.
The task “Delete Inactive Client Discovery Data” will delete inactive Devices after a defined number of days. Standard setting for this task is “deactivated” and when activated the period is 90 days.
Before setting this option you should think about the usage of your devices. Sometimes field workers or simply colleagues on holidays can easily be more then three or four weeks offline before connecting to the network again. In these cases the period should not be set to low.
About inactive devices: A device will be set inactive if it does not communicate with the SCCM server anymore. The communication can be Heartbeat, System or Network Discovery.
A corresponding Microsoft TechNet article can be found here: https://technet.microsoft.com/en-us/library/bb693646.aspx (article is for SCCM 2007, but is still valid for SCCM 2012).
I hope this helps during the next troubleshooting.