Originally posted by skatanatos
I just realized something, Your save file from the mediafire link contains only one file, which is for the collection itself. you said you activated rookie hunter mode on only save 4 of x7 which is impossible as save file 4 is within X7, Rookie hunter mode affects the collection and if it's enabled in the game itself, the save files included within the game or for that specific game is flagged as rookie hunter mode. Essentially the reason the trophy doesn't unlock is that the game is or was at some point played in rookie hunter mode.
Tested it on my alternate account. Activation of Rookie Hunter Mode only affects that particular save file. Playing Save File 3 of Megaman X7 unlocked the We Haven't Seen The Last of Them trophy. So save file 3 is not affected even if save file 4 was played using Rookie Hunter Mode.
The same thing happened when I tested Megaman X5. Save file 2 is touched by Rookie Hunter Mode. Even if I beat the game without Rookie Hunter Mode, I did not get the He Wanted You to Have This trophy since I was using Save File 2. When I use save File 1 (untouched by Rookie Hunter Mode), I was able to get the trophy.