I have been recently devoting my efforts to learning more about what SCOM has to offer to Lync Deployments and in the process. I have decided to break and test a few things, I ran into this error today and wanted to put up a quick reference to the cause and fix. This error is occuring between my Lync Standard Edition Front End and Lync Watcher Node
Error [Lync] Failed to replicate to some of the machines in the topology.
This error is pretty simple enough to understand as Replication between Lync Servers uses a TCP Port. You can use Get-CsManagementStoreReplicationStatus and this will confirm the error generated in SCOM.
The first simple test is to use PortQryUI to ensure the port is open between to Central Management Database. Flinchbot Blog Post has everything you need to be able to test this, head over to https://flinchbot.wordpress.com/2013/05/10/portqueryui-config-xml-file-for-lync/
In my case I had a issues with my GPO that managed the Windows Firewall. As soon as I disabled the GPO and the Windows Firewall on both the Lync Front End Server and Lync Watcher Node I was able to replicate the Central Management Database by using Invoke-CsManagementStoreReplication or you could let the databases replicate naturally.
You need to ensure that all the required ports are open when deploying Lync. You can find out what ports need opening by downloading the Lync Protocol Poster available here https://www.microsoft.com/en-gb/download/details.aspx?id=39968