How do I use MySQL Workbench to edit an existing, in-production database?
This is an arguable opinion, from limited personal experience.

I believe it was the Workbench who screwed up the process of round trip engineering several times. I don't remember all the detail, but it certainly synchronized more objects than had actually changed.  It silently deleted some data a few times.  And it sometimes generated SQL that the server rejected.  It was a development DB, no big deal, especially compared to the benefits.  But in production I'd rather refrain from being at such a tool's mercy.

Some other people's experience was similar, e.g., MySQL Workbench model/source synchronize issue

So for a production DB there may be risks, including that of losing your data. I would stick with phpmyadmin and do synchronization back into the model, always checking what the Workbench is going to do. Keeping the model just for reference.