Im pretty sure they are not interchangeable as kubbie said one is high pressure and the other is return. .
One is supply and the other is return, but they are at virtually same pressure (3 bar) - the return is at same pressure because is part of the same 'vessel' and the pressure regulator is actually AFTER (in terms of flow) the return fitting.
Although the manual stresses to connect them correctly, in practical terms it makes no real difference to running performance - fuel simply flows the other direction to the fuel rails but still provides the same flow and pressure at the injectors. The only other difference is that the return hose is slightly larger diameter but again makes no practical difference in terms of performance/running.
Not suggesting to ignore the advice - just that in real World there are no negative consequences.
Back to original question:
So why did Triumph use two gas lines on some daytonas and one on others.
On earlier models up to Serial # 201541 on the Daytona, Triumph used the two-line Supply/Return system to fuel rail, with the pressure regulator connected AFTER the return fitting.
This was the standard config on all Triumph FI models from 97 to about 2004.
Beyond that, the pump systems were reconfigured to a single supply only, where the fuel pressure is regulated BEFORE the supply fitting.
Again, this change affected virtually all the FI models at about same time-frame.