Um... so it turns out I did play around with element category access permissions after all. On Wednesday I was in the access controls area, noticed the element category access tab for the first time, and evidently I engaged in what we in our office like to refer to as "indiscriminate messing around". I must have granted a certain user group access to this particular category, just to see what would happen.
Then I didn’t notice anything, went home, and a major family medical emergency took up the next 36 hours of my life, causing me to forget having ever done this.
This sequence of events led to my mystical discovery today of my category having vanished, and my confidence that it couldn’t possibly have been due to anything I had done because I hadn’t done anything.
Snooping through the db I found the modx_access_category table tonight, with a record that had a number in it that matched my missing category.
I verified that this was indeed valid evidence by adding a few more element category policies and watching them show up in the table.
Darned if I didn’t see a category disappear right before my eyes when I set up a policy w/ that category + a different user group + manager context!
Dangerous stuff, this Indiscriminate Messing Around...
I deleted all the records from the table, and of course now I’m back in business.
On the bright side, I’m now extremely confident that I’ll be able to hide my precious elements from my dangerous users. (Including, evidently, my most dangerous user... me

)