When you are taking Thermal images using a drone, I am losing the values in the orthomosaic image, while they are still present in the original images.
What software are you using? All the program should be doing is correcting distortion so that the image works like a map. The other possible issue is the orthophoto is corrected so that it appears you are looking straight down, as from a satellite. This means the sides of objects, such as buildings, aren't visible so that thermo information is lost.