Hi Danielle,
If I understand correctly, you want to use the custom field filter to filter a taxonomy term result? I’m asking, because that is not possible. The custom field filters apply to custom post type results (or user results), but not to taxonomy results.
The custom field selector on the index table queries the post_meta database each time to get the custom fields. If you don’t see a cutom field in the list, that means, that there is no post yet, that contains that custom field with a value. Once you add a post or change a post, with that custom field set, it will start appearing.
If you also see fields that you have deleted, then the deletion may not changed the existing fields for existing posts. They still exist in the post_meta table, thus they still can be used for filtering