In case anyone else comes across this I was able to find what I was looking for under “Scheduled Tasks” on the left pane of the Emby server. Running this job repushed everything and seemed to fill in the handful of movies I was missing (and quite a few others apparently).
I think I’m all good on movies now, but I still have some strange behavior I’m tracking down with TV Shows. I’ve got some metadata to clean up and a few things to try then I might be back, but I’ll close this up 
