I used the XMB native function.
I was able to unlock the trophy legit in-game, and then get it to sync correctly. I don't know why that overrides the flag but it seems to have fixed it.
I really wish they didn't have that built-in functionality with zero explanation. It should have some kind...
I recently installed the latest EvilNat and saw that it had a built in trophy unlocker. I tested it out by unlocking one single trophy and then syncing. The trophy did not show as unlocked once synced.
I then deleted the folder, rebuilt database, and unlocked all the trophies in that game using...