As long as you have synched your trophies to the server there is no way to lose them. If you can see them online through your computer your good to go.
anything in the "game data utility" folder is only the data the game installs onto your system. it has nothing to do with game saves or trophies. you can delete anything inside the game data utility you want, it will be re-installed in the event you decide to play the game again but it will clear tons of memory, especially with games like metal gear solid that takes up over 5gb's of memory on your hdd.