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Actually I don't do this. I do try to keep the filters clean though to avoid dust donuts. The vingetting is very similar between the three colour filters. I have a set of flats for the L at both 1x1 and 2x2 binning, colour at 2x2.
I do need to take a set for the Ha filter as the focus is different.
Even so it's really not that much trouble as once your set and focussed it's just a matter of setting up an automated run for each filter in CCDSoft at twilight. If you keep your filters clean then the camera orientation doesn't matter either (at least in mine).
Cheers
Stuart
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