I'm also no expert in this particular topic, but the heat transfer to the surrounding material shouldn't play to huge a role. First because the material is very thin (50 nm) and second because the the X-ray focus is much smaller (5 um) so I would only probe the material in the middle of the heated spot.
The effect of the X-rays depends strongly on the intensity of the beam (which I can't figure out on mobile ATM). X-rays can definitely melt or vaporize material of this thickness when the intensity is high enough. In this case here it hopefully shouldn't affect the measurements to much.
Einfach nicht verrotten lassen. CO2 weg, wie bei der Entstehung von Kohle.