I had the same thread as you have now a few weeks ago.
After a week of struggling I found the perfect solution.
Here is how I upgraded my HDD without losing my trophies. (PS3 PHAT 80GB 16MB NAND)
1. FTP (blackbox or whatever) to hdd0\home\(userid) and copy the tropy dir to your computer.
2. OFW 3.55 (recovery menu)
3. Backup (backup utility)
4. Replace HDD
5. Install 3.55 OFW
6. Restore backup (backup utility)
7. Install CFW 3.55 Kmeaw (XMB)
8. FTP to hdd0\home\(userid) and copy back the tropy dir.
9. Go to recovery menu and choose Rebuild Database
10. After rebuild go to XMB and see all your trophies restored.
Have fun with your new HHD!!!
PS3 80GB PHAT (640GB Int.) 3.55 kmeaw.
PS3 320GB Slim 3.60 OFW.