I'm working on an add-on, frequently reloading scripts and using it to work on multiple files. After a while, doing that, Blender stopped registering some new operators, while it did recognize others.
The add-on's code had no errors, and nothing would show up in the Blender console.
Here's a picture of the problem: both are in the same version of Blender, with the same version of the add-on. In one file, the operator is available, but not in the other.