When I run recon-all on my data, some skull and dura is left behind and affects the surfaces and the parcellation.

I re-run the data using a lower watershed (I tried 20, 15, 10 and 05). The brainmask changed, but the remaining skull still affects the parcellation and surfaces. 

My doubt is: when I re-run my data using a lower watershed value, does it automatically create new surfaces and volumes or not? If not, how can I reset it?

Best

Mateus