Prime/Safe are reducing agents based on hydrosulphide salts. This is why Prime reacts with chlorine compounds, which are oxidising agents. If there is no chlorine present left to reduce it will find something else to reduce, such as oxygen. The time that it takes to completely dissipate in a closed system such as an aquarium will vary from tank to tank based on a number of factors. In your example, as long as "afterwards" is shortly after filling your tank, chances are the excess water conditioner will still be active.
