Sql-server – SQL Server is unable to connect to server , requires the actual server name

You'll want to log onto the distributor and stop the merge agent. Then open a command line window and navigate to the folder which has the replication binaries in it (c:\Program Files\Microsoft SQL Server\100\COM\ by default). Run replmerg.exe and paste in all the values from step 2 of the job which is the replication agent. Then change the -OutputVerboseLevel from 0 to 1 (the parameter may not be there if it isn't just add it was an value of 1).

This should give you the actual error message so you can see what's going on.

You need to add a CNAME in your DNS at your primary SERVER putting the DR server's hostname. This way publisher.mainsite.mycompany.com can be resolved. Then use publisher as the hostname to use when connecting.