A case can be made for doing the chip repair either way, before the correction work and/or after the correction work, but I would lean towards doing the touch-up work after the major paint polishing work is done because all to often if you buff over fresh touch-up paint you'll simply pull the touch-up paint out of the rock chipped areas.
I've see the Dr. Color Chip system in action and it was done after the paint was polished, the results were impressive appearance-wise. It would have been interesting to see if the results would hold up to machine cleaning and polishing.
One thing for sure, it's very frustrating to do touch-up paint repair work and then watch the touch-up paint be removed if you buff over it.
You could try doing the touch-up work before buffing and then try not to buff over the touch-up paint but that' usually not practical.
You could also do the touch-up work first and then cross your fingers the paint doesn't pull out or buff off and if it does, note that for the future and then re-do it after the cleaning and polishing work.
Be sure to let us know which approach you use and the results.
:xyxthumbs: