There is no way to completely reset the Digitrax DCS100 or DCS200 Command Station/Booster using Option Switches such as Option Switch 39. Option Switch 39 resets Locomotive Registry, Consists, etc. associated with DCC equipped locos by resetting mobile decoder info (that is in the command station) and consists, routes and loco roster info. It does not necessarily reset other Option Switches as expected.
A complete reset of the DCS100 and DCS200 to factiory defaults is only accomplished by removing input power and removing the battery. This involves disconnecting the grey terminal plug then removing the metal cover by unscrewing the screws on the top and bottom of the case, and removing the battery. After 60 seconds the battery can be reinserted into its holder and the unit reassembled by replacing the metal cover and reinserting the screws and then plugging the grey terminal plug back into the unit and powering it back up. All option switches will now be in their factory settings.
Since you have the case open and the battery removed, it might be a good time to replace the battery.
The battery is a CR2032 coin type cell.