Hello,
I’m trying to make some quick animations inside Unity for a 3D Model.
Before starting. I have manually Rotated some bones to reach a certain position just like this:
After clicking on the record button or even the “Preview” button in the Animation tab, the model changes position like this (the clip is still empty):
I have no idea what is the reason? what am I missing? 
Kind regards,
Most likely explanation:
Animator/animator, when fired overwrites ALL positions of all bones it controls.
In your scenario this could could be either default skinning pose, OR, more likely it is default mecanim pose. Because when you configure humanoid avatar and go to the testing tab (or whatever it is called), the model will be posed like this.
By the way, I do not recommend animating things in unity, because it uses euler angles for rotation, which makes animating rotations painful.