Most fan leaves should not be removed, none per plant per day.
The large fan leaves are the energy producing solar panels. Large fan leaves can be removed sparingly if they are blocking a significant branch, which may have a bunch of leaves itself and potential flower developing sites or flowers, but otherwise do not cut off your fan leaves. Depending on how many nodes tall your plant is, you might top it, depending on your style of training/pruning, but otherwise you almost never want to cut a lot of healthy parts of the plant off.
As far as when, yes it is actually best to prune and train a little bit before the lights come on. This of course requires a special green light so you can see what you are doing without interrupting the dark photo period schedule. even the little bit of light from opening the door or what have you is not good for the light schedule, so no light at all should be leaking in during the dark period. If this is too troublesome, then the pruning or training is best done right after the lights come on, this gives the plant the entire rest of the light period to grow, heal and repair before the following dark period, when wounds will be more susceptible to diseases like mold/fungi.