Stealth aircraft are designed to absorb most of the microwave radiation that hits them and to reflect whatever they don't absorb away from the microwave source. That way, any radar system that tries to see the aircraft by way of its microwave reflection is unlikely to detect anything returning from the aircraft. In effect, the stealth aircraft is "black" to microwaves and to the extent that it has any glossiness to its surfaces, those surfaces are tipped at angles that don't let radar units see that glossiness. Since most radar units emit bright bursts of microwaves and look for reflections, stealth aircraft are hard to detect with conventional radar. Just as you can't see a black bat against the night sky by shining a flashlight at it, you can't see a stealth aircraft against the night sky by shining microwaves at it.

Like any black object, the stealth aircraft will heat up when exposed to intense electromagnetic waves. But trying to cook a stealth aircraft with microwaves isn't worth the trouble. If someone can figure out where it is enough to focus intense microwaves on it, they can surely find something better with which to damage it.

As for detecting the stealth aircraft with the help of cell phones, that brings up the issue of what is invisibility. Like a black bat against the night sky, it's hard to see a stealth aircraft simply by shining microwaves at it. Those microwaves don't come back to you so you see no difference between the dark sky and the dark plane. But if you put the stealth aircraft against the equivalent of a white background, it will become painfully easy to see. Cell phones provide the microwave equivalent of a white background. If you look for microwave emission near the ground from high in the sky, you'll see microwaves coming at you from every cell phone and telephone tower. If you now fly a microwave absorbing aircraft across that microwave-rich background, you'll see the dark image as it blocks out all these microwave sources. Whether or not this effect was used in the Balkans, I can't say. But it does point out that invisibility is never perfect and that excellent camouflage in one situation may be terrible in another.