How do TV shows with live audience manage special effect scenes?

From the Wikipedia entry for the Bodyswap episode:

This was the first episode to be recorded without the live studio audience. Technical difficulties of the actors playing other characters meant that the scenes would have to have been done twice. Instead the voices were dubbed over the scenes in post-production and trying to match up with lip movements caused much mirth while recording. Chris Barrie, being an impressionist, had no problems playing Lister, whereas Craig's portrayal as Rimmer was not as smooth. The final edit, with dubbed voices, was then played to a small audience to provide the laughter track.

This is a common technique for scenes that can't be recorded with a live studio audience:

In the 20th century, most U.K. sitcoms were taped before live audiences to provide natural laughter. Scenes recorded out of doors, traditionally recorded in advance of studio work, are played back to the studio audience and their laughter recorded for the broadcast show.

I was in the live studio audience for the taping of a sitcom maybe 15 years ago when I was living in southern California. There was a scene that couldn't be done live (no special effects; I believe it was just a scene outdoors). It had obviously been taped beforehand. The regular "set" consisted of the interior of a house -- laid out horizontally so each of the rooms had one wall missing, all facing the audience.

Scenes for "live" sitcoms are taped in chronological order, otherwise the audience would get pretty confused. (Sometimes if the actors made a mistake, they would have to redo the scene. The hard part then was to get the same reaction from the audience -- if they didn't I imagine they had to "fix" it during post-production.)

When the outdoor scene came up, they stopped the action on the set, dimmed the lights, and played the scene on several large TV monitors spaced across the front of the full audience. (In fact when I first sat down, I was wondering what those were for.)

I actually managed to see an episode of Red Dwarf being filmed (Siliconia, series 12 episode 2). This is a pretty effects-heavy episode, at least with various characters having the Kryten/mechanoid make-up applied.

The standard Red Dwarf studio set for series 12 consisted of the bunk room, some corridor sets (including one going behind the bunk room and guest set, out of view of the audience), a "guest" set (which changes from episode to episode) or the science room, and Starbug. In our case there was also another set in the corner which was built upon and changed.

The episode takes place on a ship populated by mechanoids, for which a large amount of make-up is required, and our heroes get transformed into mechanoids too. In order to film this, there was a large amount of extras there wearing the mechanoid make-up, but the heroes are in their traditional outfits/look. For the scenes where they are in their mechanoid bodies, these were recorded beforehand and shown to the audience on large monitors (which show all the action being filmed anyway, in case audience members cannot see - I had a large camera assembly in front of me, for instance, so couldn't see much of the action). The scene where the heroes are transformed into mechanoids was filmed a few times live, and the counterpart where their mechanoid bodies revealed recorded a few times, in order to get the best reactions to both, where I assume they used split screen techniques in order to get the desired results.

For space shots, we were shown storyboards and had various stand-ins (the Death Star sporting a Divadroid logo was a popular one), or in the case of Lister's guitar floating through space, a greyscale CG render. Other things are applied afterwards - there is an out-take from a previous episode (series 4's Meltdown) where Lister (Craig Charles) knocks on a wall, pretending it to be stone. From the sound it is quite obviously wood and he explains to the audience that "they were going to sort that out in the dub".