So I think I found the stupid problem with boards not being pushed. One of the developers added code to the database config to they wouldn't have to set the production/development environment in the proper place. They based it on the $_SERVER['SERVER_NAME'] == 'localhost' environmental variable. Problem is two fold. First, the dev site is a NGINX reverse proxy in front of a LAMP stack, so DEV is also called localhost and had wrong database settings. Second, all the cron jobs were failing with errors because $_SERVER is undefined when running PHP from the command line.
Fixed VDP cannot access closed PCB area.
Also fixed incorrect order total in order display and a number of other small things.
Will update server and test the push process. After we clear all existing orders I will put the site back online.