GaryP:
I don't understand your why you guys keep saying such a thing.
Because you ask the wrong questions.
GaryP:
Simple example could be, that I wan't to avoid calculating difference between counter and external input.
So instead you prefer to mess around with linker values so that you can access the right variable and then also add the appropriate assembly instructions so that you don't get variable corruptions in case of simultaneous access by the ISR function. If you know how to do that on your own, that may be a useful option. But if you don't, messing around in that area is so completely out of your depth that nothing good will come from it. It's a just like cutting you arm off to clean your nails simply because you don't like bending your elbow and you come and ask how best to cut your arm off.
GaryP:
I take your answer as you don't like the idea, but it won't help me.
No, it has nothing to do with liking, it's all about knowing. I know that someone asking a question like this shouldn't do it. That's experience speaking. If you had a valid reason to reset the micros() timer, you'd ask completely different questions.
Korman