Unless there is a malfunction in the memory section - yes - it will remember the settings from running Audyssey and user settings as well. It may not remember you switched from 5.1 to 2.1 music but thats easy enough to turn back on.
You might want to make sure the subwoofer is on during Audyssey setup. It should detect it during the setup process. It is possible to remove the subwoofer in the manual setup menu. If that has been done the subwoofer may not be queried during the Audyssey setup.