This is to document this for others as it is a big deal for us.
There is a FEATURE that the act of re-installing the agent on linux while the machine keeps the same name causes multiple instances in the SEC database. This can cause the "New" machine to show up in the Unassigned group rather than the AD group it was meant to.
This can only be solved by running an SQL across the Sophos Database, and must be done each time the agent is re-installed, machine re-imaged or re-installed
This is different behavior to the windows client that does not have this issue.
Grant
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