Fields Missing. Gone from Database as Well as Control Panel
It sounds like something/someone is updating which could be causing the migrations to run and then subsequently fail... that could cause data loss but that's hard to say or know exactly.

When this sort of thing happens, you should be reverting to a last known good backup and then figuring out what went wrong.

That's going to be the only sane way to debug this. I wouldn't try to push something locally onto a bad state on production unless you overwrite everything (which is a hail mary move to restore to a good state).

Are you using Craft 3? The Migration Manager plugin is now called Migration Assistant. Make sure you're using updated versions of the software, as old versions can cause weird issues.