Do you have existing thermal descriptions for the device(s) of interest? Or are you trying to generate the loss models yourself?
In PLECS the IGBT and boost diode in a boost converter are independent both physically and from the on-time perspective (since the diode is ideal there is no reverse current at turn-off). But if you knew the magnitude of your reverse recovery current you might be able to add that during the IGBT conduction interval or artificially modify the Eon data to include the additional effect from the diode.
But perhaps you can provide some more background info so we can try and give you more specific feedback?