I also tried 2 different checkboxes fields, one where I left the value to the fields as "1" (default) and another where i named the field values. Both do not show up.
While waiting for a response, I also tested with an Advanced Custom Fields (ACF) "Checkbox" field as it has the same functionality I'd need. Unfortunately it does not show up in the custom search filter drop down either.
I created a new view as a test and can now see the checkboxes custom field. My existing view still cannot see them.
I'm guessing this is a cache problem but I do not see a way to clear a view's cache. I do see a "Frontend output cache" on the views admin page but it says "not cached".
I feel im close to solving this but since my view is so heavily customized, id rather not start from scratch.
Sorry it has taken a while to get back to you, there is a busy spell in the queue.
So, in the original View you cannot insert a filter for the checkboxes field, but you can if you create a new View, is that right?
Unfortunately there is no other cache that you can clear, only the front-end cache for the View output, which wouldn't be a factor in what you're describing.
I'm not sure what to suggest might be the cause of the issue on the first View given that it works in another context.
I'm sorry but there's not much I can suggest other than deleting whatever filters you have added to the search block and then recreating them.
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