Hello,
In the process of tracking down all the vacuum leaks on my S4, I tested the small diaphram which controls the top 2 butterfly valves on the throttle body. I found it to be leaking pretty bad, so now I'm wondering how this would affect things. It appears to be controlled by what looks like a water temp device of some sort on the rear of the TB. I have the vacuum line plugged until I can replace the diaphram and I'm not really driving the car yet, since I have other things to accomplish...radiator flush, brake pads, etc.

Jeff

 

I'm pretty sure that they spring open when no vacuum is applied, I believe that they generally remain closed during warmup. If I recall their purpose is to limit performance during warmup by restricting the ammount of air the engine is able to receive until properly warmed up. I believe they did this to kind of hinder the tendency of people to WOT run the car as soon as they pull out of the driveway. I'm pretty sure that with the line capped that they'll just remain open and you won't really notice anything.

 

^ what he said. cap it and it should be fine. you can cap the diaphragm and then the two nipples on the water thermovalve.

 

If you're going to disable the diaphragm, you may as well go ahead and remove the throttle plates it controls.
This is commonly called the "throttle body mod" and involves removing the diaphragm, throttle plates and thermovalve (NOT the thermowax) that controls them. The spindle holes are easily plugged with 1/8 NPT plugs.
You may notice slightly crisper throttle response after doing this.

 

I did exactly that on my S4 NA engine. The diaphragms almost always fail, so removing it and the outer set of secondary throttle plates cleans up things a little.

Also, just an FYI to anyone reading this; the double throttle system works differently on TIIs and S5 NAs. On S4 NAs, it's just a warmup related deal, as ifryrice described.