I'm also considering capturing some flats, but am still unclear on a couple of things:
1) Using a cooled camera, do I need to cool to the same temperature for flats as I do for darks?
2) I see that the image train needs to be left unaltered from the time the flats are taken until they are used. I usually remove my FR/Spacers/Camera and store them separately. So I'm guessing my only options are to either a) start storing my optical system intact or b) take new flats during the day before an evening that I'll be imaging.
As the gain is set to 0 and the exposures may be 10s of milliseconds, cooling not really needed