According to Moodle Docs, this can be done.
"Categories can also be created or deleted at will. However, if you try to delete a category containing questions, then you will be asked to specify another category to move them to. You cannot delete or move the last category in any context, there must always be one category in a context"
https://docs.moodle.org/39/en/Question_categories#Deleting_Categories
The category has no questions in it.
I think I may have more than one top-level category, and this causing real problems. When I try to restore a course I get: "The backup file contains more than one top-level question categories for context 396."