Like i said i tried this method 3 times already with 3 different games BL2, Minecraft, and Limbo and it works perfectly basically you'll want this if you don't want any trophies from pirated games to be synced to your PSN profile this is what you should do lets use Limbo as an example here :
1- Delete the game
2- Go to ur0:user/00/trophy/conf/ and choose whatever file for whatever game you want to delete the trophies for
for Limbo it'll be NPWR04612_00
3- Now go to ur0:user/00/trophy/data/ and delete the file wich will be the same name as the last one
4- Now for the last file you're going to delete you'll find it in ux0:user/00/trophy/conf/ the same folder name as above and delete it
5- Now exit vitashell and go to Trophies app and the trophies for the game should look like this
6- Exit the trophies app and open it several times and the trophies should be gone
this wouldn't be doable without Vitashell so all thanks to TheFlow
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