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.