Sync Users Manually (via phpmyadmin or adminer)

I have a userbase of over 360k users that I need to sync. Every time I hit the sync button, it syncs for about 5 minutes and manages to sync about 2.5% of my user database before crashing. A few minutes later, my site is back up, so it’s mostly fine.

The problem is that to sync 100% of my user base, I’d have to do this about 40 times and that will not only take long, it will also cause downtime and crashes every 5 minutes, which I can’t afford.

I am comfortable manipulating data via phpmyadmin, so I was wondering if there was a way to manually sync users that way.

So I guess what I’m asking is: what does syncing users actually do in the backend (so I can replicate it myself manually)? Does the syncing involve anything else that is not database-related?