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I would expect that you could get away with leaving it at Kindle all of the time. The worst case would then be that in some cases graphics are not optimised for the (larger) resolution of the iPad screen - but they should still display fine.
That is what I do where I want MOBI files that work on a Kindle 3, a and EPUB files that work on a Sony PRS950 and an iPad. I have not noticed any real problems with this approach.
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