These are quite modern bi-mode multiple units which only entered service in 2014, so there wouldn't be any issue with the engines being biodiesel compatible.
Using B100 is the part that's a little interesting, since even the low lying areas of northern France (where this phase of the trial is taking place) can have winter temperatures cold enough that they would have problems with viscosity. I would guess that these units already have electrical equipment to warm the fuel tanks when either running from overhead or hooked up to a depot shore supply, in which case it would be as simple as adjusting the temperature ranges used.
The article details the impacts on performance and emissions, as well as pointing towards the economic side of it. Looks like a pretty clear decision to me.