If you run the Automatic setup, which will do the YPAO measurements, then YES, it will reset everything. If you go into the Manual Setup afterwards it will not reset the YPAO/Eq settings, or any other settings, although they can be adjusted. There you can also adjust, if required, the Speaker size, layout, Distance, Level, etc. Additionally you can Save and Load a profile.
The YPAO setup cannot be done via the Manual Setup, it must be done by the Automatic.