Sometimes entire episodes have been scrapped for various reasons. Often it's due to technical problems that didn't become apparent until after the episode was recorded, but sometimes we all just decide that the episode wasn't that great and could be redone with better material. One example is the scrapped otakukin episode. It was my fault really, because I put it together and I was trying to use very, very old material from the dawn of the otakin movement. Thing is, most of the good stuff was long gone, and what I did dig up was okay, but not stellar. FUN FACT: The girl who claimed to be Ken Ichijouji from Digimon and felt SUPER ASHAMED OF HER SINS AS THE DIGIMON EMPEROR was still around! Anyway, the readings were all right, but the energy never ramped up and the commentary consisted more of uncomfortable "what"s than actual jokes. So we just tossed the whole thing and I promised myself that I'd come back to the topic some time. "Fictionkin" (as they now call themselves) are still around, but it seems most people who claim to be fictional characters now do so through "fictive headmates," so the multiples episode is kind of the spiritual successor to the trashed otakukin recording.
As for how much gets cut, it kind of varies. The classic literature episode is almost uncut because Boots stopped us after about an hour and said "I don't want to cut any of this, so let's quit now." By contrast, the Paula Deen episode was originally about 2 and 1/2 hours because we were really unfocused and rambly in our jokes, plus we read a bunch of extra shit too. On average I'd say these days, recordings are about an hour and a half, and we edit out about 30-40 minutes of them.
Also you all need to worship me because I'm the one who dug that 2+ hour long monstrosity out of the trash and edited it down into an episode after everyone forgot about it. WORSHIP ME, YOU HEAR?!