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Due to the nature of the conversion process, this might not be possible. Calibre will internally convert to an intermediate XHTML stage and try to preserve as much formatting as it can, but depending on what the input and output formats support, this might result in some loss of formatting. Your best bet is to try and see what happens.
Your output profile should be something that properly sets the parameters for the device you'll want to read on. I don't know what the best output profile for an iPad would be.
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