We have one primary server and two secondaries (no cas).

I recently successfully upgraded the primary to R2.

When trying to upgrade the first secondary, it failed the pre-req check because the initial SCCM 2012 SP1 install only installed SQL Express 2012 RTM on the secondary.

So I installed SQL 2012 SP2 patch on the secondary, after which the replication failed. Its important to note the network connection is international and not reliable between this secondary and the primary. 

Is there anything I need to do to the next secondary, before patching SQL (before i can upgrade it)? Do i need to stop the SMS service? Stop the SQL service?

OK, so on the second Secondary Site, i stopped the SMS services, updated SQL to SP2, that worked fine, the machine was rebooted to bring services back up.

There were no issues with the replication following the SP2 upgrade.

Since running the upgrade of this secondary site, the exact same thing has happened - Following the pre-req checks, the site does not upgrade and that process breaks Site Replication fails.....

What a very frustrating process.

There is ZERO documentation for the upgrade of secondary sites, the only mention of this in the Technet documentation is " use the Configuration Manager console to upgrade secondary sites " - It doesn't even say how or where. Very unimpressive.

This article explains the upgrade process, indeed mostly about primary sites, but also about the steps for a secondary site: https://technet.microsoft.com/en-us/library/jj86569