I just used a save game from this site about a week ago. It still works just fine and is not patched (never will be in my opinion). I used this one:
"Added: 01-13-09"
Description: 100% items, all levels aced, story mode and MGS pack
I works great! I just wanted to build levels and did not have the time to unlock all the items.
I have been playing online with the profile I created with no problems. Take a note though:
1. You have to accept their online agreement everytime you go online.
2. It always warns you are using a profile from another user and you cant unlock any new trophies.
3. It also tells you it is okay to use or "proceed" with the profile.
As far as trophies once you get them you don't loose them as far as I know. I don't care about trophies much so I will check with one of my accounts. If I dont post again by 2am then the answer is--you don't loose them. otherwise I will post