You can also delete them by... deleting the folder where are stored that files (under dev_hdd0/home/********/trohies/NPWR12345...)
After the deletion you need to enter recovery menu and use the option "rebuild database"
To find the name of the trophy folder... you need to take a look at the filename under USRDIR/TROPDIR/****.TRP
That "TRP" file is the trophy instaler, and have the same name of the folder that is going to be created when the trophies are installed
*Btw.. incase you have the trophies synced with the online sony servers this kind of deletiong works... but the next time you sync the trophies the servers are going to create the files again in your PS3