What happened to the civilian aviation engineer from the Pegasus? Was he killed in an episode and I've just forgotten?
The "civilian aviation engineer" is Peter Laird from the Pegasus first replaced Tyrol as deck chief under orders from Admiral Cain - this is temporary and Tyrol is reinstated once Adama regains control of the fleet.
In season 4, Tyrol is demoted to specialist and Laird takes over as deck chief again until the mutiny led by Gaeta when he is killed by Zarek.
I think you're talking about the guy explaining that he's been the engineer who designed some specific model of engines? I don't remember him ever being shown or mentioned again.
To me he's been there just to support the fact that Pegasus had several civilians from "its" left behind civilian fleet. It's been an easy way to introduce this on crew level by the conversation between him and Tyrol raising some suspicion, while also showing that (most of) Galactica's crew treat everyone equally in contrast to Pegasus (where civilians were replaceable "tools" to fuel the war efforts).