When editing a Sim's Body Flags on SimPE, if that Sim is pregnant (in any stage) and I select Fit, what happens to the pregnancy?

Nothing. Fitness and pregnancy have nothing to do with each other. Fit means the Sim is in the upper third part of the fitness meter, although I don't believe the meter will max out by checking it. I'm guessing it's about turn-on flags.

The boxes with pregnancy in the name will affect how the Sim looks. The highest trimester that is checked is what they will look like. I forget the names of the boxes, but if 2nd and 3rd are both ticked, then the Sim will show as third. If only one is ticked, that's the one they look like.