This is something I’ve been struggling with for some time now.
I also saw some clients appearing and vanishing from the console at, what seemed, random times.
I was experiencing that most WSUS clients were not showing up in my management console. When looking at the logs I didn’t see anything strange, nor did the eventlogs of Windows tell me anything useful.
So, I downloaded the Diagnostics tool for WSUS from SolarWinds. Unfortunalty it didn’t report any problems whatsoever.
So after a lot of searching I’ve found the cause. As it seems the previous IT guys rolled out new systems through a cloning process.
WSUS clients are identified through an ID which is located in the registry of the WSUS clients. Each key needs to be unique!
So it seems they didn’t remove the WSUS ID’s when creating the clone.
It concerns the keys ‘SusClientId‘ and ‘SusClientIdValidation‘ which are located at ‘HKLM\Software\Microsoft\Windows\CurrentVersion\WindowsUpdate‘.
To remove these keys, the wuauserv service needs to be stopped first. After the deletion of the keys, the service needs to be started again.
So, here’s a small script which does that:
net stop wuauserv reg delete HKLM\Software\Microsoft\Windows\CurrentVersion\WindowsUpdate /f /va net start wuauserv wuauclt /detectnow /reportnow
Problem solved 
