Page 28 of my manual says flipping S2 up and down 5 times resets the current location of the quad to a new home point
The fast green blinking lights is the confirmation a homepoint is set, both automatically and if reset by the above option. The page 28 you refer to is to reset to a new home point... Many people use the feature to set a homepoint well overhead in case of varying elevation, like hills, for a RTH event. The new homepoint would be set at that elevation to 0,0. And even if you were 399 ft. below the HP, the craft would properly descend and land once it senses no further reduction in altitude.