By default, Lync saves conversations in an Outlook folder. This can be changed on the server by running:

Set-CsClientPolicy -Identity global -EnableIMAutoArchiving $false -EnableCallLogAutoArchiving $false

And everything is fine… on the client, the options change from one state to another.

The question is whether this can somehow be done through GPO with filtering. I would like to be able to set it differently per user, so that it is disabled on some workstations and not on others.

The Lync 2010 policies are a bit thin… (Microsoft Lync 2010 Client Group Policy Documentation).

Fortunately, policies from good old Office Communicator still work ;-))) and among 75 other settings there are two that interest us… (Microsoft Office Communications Server 2007 R2 Client Group Policy Documentation).

As a curiosity, this change can also be made through the registry by editing or creating these keys:

HKEY_CURRENT_USER\Software\Policies\Microsoft\Communicator\ImAutoArchivingPolicy (DWORD, 0 - disabled, 1 - enabled)
HKEY_CURRENT_USER\Software\Policies\Microsoft\Communicator\CallLogAutoArchivingPolicy (DWORD, 0 - disabled, 1 - enabled)