You can start counting your 3 wks from the day you water is in hyposaline conditions--1.009sg and 14ppm salinity. To be on the absolute safe side, I think it is best to start counting from the day the fish no longer have symptoms. This allows for a margin of error, particular with hobbyists who are not familiar with the hypo procedure.
This assumes that the hobbyist follows the instructions in the FAQ thread exactly.