When I notice that I qualify for a challenge cache, I ususally use the corrected coordinate feature on geocaching.com to mark them as such together with a personal note.
On the map of challenge caches I can identify the caches I already have noted as qualifying by looking for the "personal note" pen on the cache icon. Would it be possible to add a filter so that I can easily hide those caches? That would make it a lot easier to find challenge caches that I haven't identified as qualifying yet.