I recently experienced an issue with a very large number of ConfigMgr 2007 package updates (400) to a large number of sites (1700). It turns out there was already a distribution job that was “stuck” in the queue and when the large update went out it resulted in a massive backlog. The end result being there were over 1.3 million files in the Replication Manager inbox that just weren’t being processed, and the number was increasing.
The only option in this sort of situation is to stop the services, move the files out of the inbox, let normal inbox processing resume and then copy the files back in a block at a time. In this case doing this manually wasn’t an option due to the number of files, so I resorted to a quick script based on the one found here: https://tricksntreats.wordpress.com/2010/05/30/sccm-backlog-fighting/