I've used "Cool Edit" to do exactly this, when I was actively involved in Production work at WFIF. :) I did, however, find a method where the find/remove silence *DID* result in not only a usable product, but a natural-sounding one. :) Finding any silence longer than 750ms, and limiting them to 750ms seemed to be the "sweet spot". ;) It worked VERY well at reducing 31 minute files to the necessary 28 minutes. :)
It took a bunch of trial & error with MANY do/undo cycles to come up with that 750ms setting... but I share it willingly and gladly. :)
As for scanning for dropped moments in LONG recordings... Cool Edit (Adobe Audition) will do that nicely, with the right parameters.