It looks like I've run into a limit on batch size for the web sync using 2008 R2. I'm getting the following error the log.
2015-02-25 16:27:42.325 The format of a message during Web synchronization was invalid. Ensure that replication components are properly configured at the Web server.
According to the following post I need to use pre-computed partitions in order for theWebSyncMaxXmlSize registry setting to have any effect.
http://blogs.technet.com/b/claudia_silva/archive/2011/05/12/replication-unable-to-synchronize-subscribers-via-web-synchronization.aspx
I did not setup any partitions when creating the publication or enable the pre-computed partition setting. If I change the pre-computed option to true and rerun a snapshot do I need to re-init all the subscriptions? Are there any other settings I need to modify to get around the size limit?