Dealing with archived caches
Gary and I got bit by this one time in NH when we kayaked to a location, looked for a long time, gave up, drove home, only to find the cache was archived months earlier. That's when I found out that once archived, the cache no longer shows up in PQ's, except for a "My Finds" PQ.
From the GSAK support forums, the suggested way of dealing with this is filter your cache list using the Last Update GPX on the Dates tab of the Filter. Change the dropdown to "On or before" then enter a date earlier than your earliest PQ.
For example, if you only have one PQ running on Mondays, set the filter to the Sunday before the last run.
For me, I have a set of queries that run over the course of a week. I don't have any that run on the weekends so each weekend I set a filter to the prior Saturday, and uncheck the "Found" Found Status on the General Tab. Everything remaining has been archived so I delete all waypoints in the filter.
Be careful not to select a date in the future! You'll wipe out all your waypoints until you process the PQ again. For my own sake, I always double-click at least one waypoint to open the waypoint in my browser and double-check that the cache is archived before I delete the ones in the filter.
Make sense? It seems straight-forward to me but I know my explanations are not always so.