If a skipper swaps boats with another skipper during a days racing do you score the boat number of the  skipper?  I think I know the answer but would like confirmatiion.

The correct answer is that you should both be disqualified as you cannot change the hull during a series.  What you do via a gentleman's agreement at a local level is up to you.

In the case of 10Rs that have multiple certificates for the same hull (yes this is a ludicrous rule), you can only sail under one certificate in a series.