"TargetRegistrarPool" with identity "12345678" assigned to "sip:user@mydomain.com" has been removed from configuration store.

It looks like the Registrar Pool associated with the user has been removed from Lync/SfB topology, but the user's attributes are not yet updated. To resolve this issue, follow the steps listed below:

Find the user in Active Directory OU
Go into that Active Directory OU
Open User's Properties
Select Attribute Editor
Find attributes as listed below and Set to "Not Set" or click on "Clear"

• msRTCSIP-FederationEnabled
• msRTCSIP-InternetAccessEnabled
• msRTCSIP-OptionFlags
• msRTCSIP-PrimaryHomeServer
• msRTCSIP-PrimaryUserAddress
• msRTCSIP-UserEnabled

Once done, check again Lync and there should be no more warnings.