First of all I needed to resolve the conflicts, which I did manually (there weren't all that many)

Then I just manually started a synchronisation via Replication Monitor > Subscription Watch List > double clicked the appropriate subscription and just set it off from the Actions menu

You should just be able to kick of the job under SQL Server Agent jobs from the Publisher also (assuming it's a push subscription)

Or do you mean how did I re-synch in the scenario that a replicated table does not have the same records in it (Subscriber compared to Publisher) even though there is no row filtering occuring? I had this happen to me too, so just trying to figure out what the problem you're having is