We have a custom type with a custom taxonomy. We use a search filter to filter the type of flowers that we show, but there are two categories that we don't want to show in the radio buttons list (to filter): Undefined (that still says there is one item in it, though it seems to be empty) and Christmas (that we'll probably reactivate in fall)...
So, we created a query filter to show all taxonomies, except those two... but it doesn't take it: i.e. they still show in the list in the seach... How can we get rid of them (if it's not through the Query Filter)? Why does the Search feature seem to overwrite the Query Filter?
P.S. In case it wasn't clear, we created a Query Filter with the option, for the Category taxonomy, "No one of the following" and we selected "Undefined" and "Christmas"... So, our expectation was that these wouldn't show in the filters... Not only do they show, but if we select "Christmas", it does show them (instead of an empty result, due to the Query Filter)...
The settings you chose are only for Query Filters and will not influence Front End Filters.
You should indeed only edit a Query Filter when you do NOT have any Front End Filter.
The query filters are otherwise automatically generated exactly with the settings as passed and required for the Front End Filters.
The only way to control the options output in a Front End filter is by using Custom Values in the Front End Filter when inserting it in the Views "Search and pagination" section.
But this is only possible for custm fields, not for Taxonomies.
Right now, it is not possible.
You'd have to remove that taxonomy term to have it not appear in the front end, or use Custom Fields, which allow such controls by adding manual values in the filters when using certain input mode (select)
Since you are a contractor, I can badly redirect you to contractors for custom code help, which is the only other way around this limitation 🙂