Hi Oscar,
SSPs are defined at the sensor level and therefore are independent on the head position. So yes you can adjust the head position after computing SSPs.
In a little more detail, when you say:
I presume that refers to options when creating the brain/head surfaces. And then you adjusted the co-registration with "refine head position using head points" again. In that case, indeed simply doing "refine position" on the filtered conditions would be the simple solution.
P.S. I recommend also adjusting the head position based on continuous head tracking, as explained in the head motion tutorial.
Cheers,
Marc