I've had the same problem and finally came up with a solution, not an easy/quick solution, but one that at least works. No credit to myself; I had to probe my local geomentor's mind for this.
Assuming that you have Easy GPS installed on your computer, and that Garmin Spanner is "on." Also, my geomentor suggests backing up all your waypoints in Base Camp before fooling with this.
1) Connect your 62s to your computer with the USB cable.
2) Choose "Yes" for mass storage.
3) On your computer, click "Start" and choose "Computer."
4) Click "Garmin GPSMAP62s."
5) Open Garmin folder.
6) Open GPX folder.
7) You should see all the geocaches in your GPSr. If you've loaded via pocket query, they should be at the bottom, labeled "Send to GPS (date)." If you loaded them directly from Geocaching.com, they should be listed individually. (Saved routes are here, too.)
8) Open any geocache or pocket query to clearly identify it. Then return to the listing and right click, Delete whichever ones you want to get rid of.
This is kind of clumsy if you have hundreds of caches to delete, but hopefully if you have that many, you loaded them via large pocket queries and therefore can delete whole pocket queries at a time. If you want to keep the unfound caches in a pocket query, the only thing I can think of is to delete the whole pq and then make another pq with the same values, except exclude "found caches."
I'm definitely NOT an expert, but I feel your pain, and I hope this helps.