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I often convert epubs to mobi and I haven't come across any issues related to the conversion yet. By that, I mean that any formatting issues were present in the epub file and not a result of the conversion. I use Calibre for the conversions.
The reason I do so many conversions is because of Smashwords - their "Meat Grinder" churns out decent epubs, but the mobis offered are often lacking in metadata, cover, formatting or all of the above. So, I download the epub and do my own conversion and get much better results. And I also like to shop at B&N sometimes, so those obviously need conversion.
There are format differences that could affect specific files, but I haven't come across any yet.
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