The new Package Transfer Manager (Pkg Xfer Mgr) component performs the distribution of the content but the distribution manager still processes the distribution jobs.
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/ I first had this happen on just one of my servers.
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.
I don’t want to be blamed that content gets removed from your distribution point while you are cleaning things up. Removing content from a distribution point while initially deployed to a distribution point group is evil! If you remove a distribution point from a distribution point group, the content stays on the distribution point.