Even after the Hero of Time is sent back to his childhood, TWW, in the theoretical adult timeline, has the Triforce of Courage. Twilight Princess and other games, in the theoretical child timeline, has the Triforce of Courage.
If the Hero of Time no longer exist in the adult timeline because he went back to his childhood and changed the future, then the Triforce of Courage and the Master Sword would have to either be in one timeline or the other.
Or so I thought.
In Majora's Mask, your Hero's Shield can be stolen. If you play the Song of Time and travel back to Day 1, you will have your shield again. Theoretically, the same principle applies to the split timeline. Before getting sent back to the child timeline, Link gives Zelda the Ocarina of Time. Theoretically, he could leave the ToC and MS in the adult timeline, then when he arrives in the child timeline, he will have the ToC, MS, and OoT. That would theoretically "clone" the ToC and MS (and maybe the OoT if a future game in the adult timeline uses it), leaving one copy of each in each timeline.
Also in MM, Link can get a bow, go back in time to before he obtained the bow, and he will still have it. The same applies to the ToC in theory. Even if he is sent back before Ganondorf entered the SR and touched the Triforce, he would still have the ToC.
What is it that makes people think the Triforce of Courage or Master Sword actually went back in time with Link? Link didn't even bring back his own left hand, why would he bring back anything else? The way Marty McFly travels through time, the hover board would go with him. But when Kate Pryde-Rasputin was sent back into young Kitty Pryde's body she left behind everything that was in the future (sorry, can't think of any notable possessions.) Had young Kitty received a dragon necklace sometime before Kate entered her body, the necklace would remain with Kate in her body. If Kate had also received a dragon necklace at the same time young Kitty had, that necklace wouldn't have gone back in time with her, it would remain in the future with her body, but she would still be wearing it when she entered Kitty's body because Kitty was wearing it anyway. Throw in the Majora's Mask rule that allowed Link to have the Bow before he received it (which was now mysteriously missing from the chest) and Link can have the Triforce of Courage even before he received it in the past.
To reiterate, if Link's left hand doesn't go back in time with him, there's no reason to think that whatever was in his left hand would go back with him?