No, biodiesel is actually better for your engine. It is a solvent and a lubricant, as well as a fuel, so it will clean out a system that has been running petroleum diesel, and it will provide lubrication for your injection pump and other parts. The ultra low sulfur diesel that is available now has less lubrication (that’s what the sulfur was for) so it is hard on engines that weren’t designed for it. Even running just a small percentage of biodiesel mixed with regular diesel will allow your engine to run with better "lubricity".