They don't have to replace the diesel engines, they just need to fill up with biodiesel. (Or convert the engines to use ethanol instead, which I've seen somewhere not being very complicated.)
That would depend on how much diesel they are currently using.  I've been critical of bio-fuels like ethanol and biodiesel mainly because, at least here in the USA, we won't be able to make nearly enough of either to replace the amounts of gasoline and diesel that we use, but the general public doesn't know this, so there is this false hope that there is no need to prepare for less energy in the future.  (Soil depletion and letting people elsewhere starve so we can drive also factor in to my criticism.)  I am not against any use of biofuel, I just think it needs to be done sparingly and carefully.

Unfortunately I have no idea how much diesel fuel France's rail system requires so I can't say if it would be possible for them to switch their rail to biodiesel.  I have only looked into automobile fuel in the US so far.  If anyone knows more about that, they could shed more light on the feasability of biodiesel trains.