Methyl Ester (biodiesel) will swell low grade rubber over time, so there is concern with certain O rings and hoses over time so I would have it in the back of your mind, but its still something that I am not overly concerned with. The O rings that would possibly have issues would be the ones in the quick connects on the fuel lines. The Injector O rings from what I know are silicone so they are not as affected.
Warranty, would be something in question, and is also subjective with the dealer. If its under warranty I would use caution for the fact that they may give you hassle about it.