Hi!
Are you sure that those are custom fields indeed? If so, they should appear on the settings page.
Do you know the names of those fields? They might be set to private and have an underscore “_” character before their names.
There is also a limit for listing custom fields on the search options page, but it’s set to 500. I counted the items there with javascript, there are 242 fields there currently, so it’s not that.
If you tell me the names of the custom fields, I might be able to investigate why it’s not there.