This happened to me when i deleted all my Bioshock info from my system after getting a few of the early trophies. After i re-installed it would always give me the 'toaster in the tub' trophy and when i would check the list it would say it was the only trophy i had. Although after re-syncing with the server it would always correct my list to what it should have been.
If you synced your HR trophies with the server they should be safe, if not I'd try and get one of the easier trophies to see if you can 're-earn' them or if they have glitched.
Should just be a case of re-syncing your list with the server though?
I've had this happen with quite a few of my games. Like Doc says, it's nearly always after installing the game data or an update. LBP is a frequent offender.
If you've synced with the server then you should be okay. On the odd chance that they don't reappear (happened me with some RFG trophies) they should still be included in your total amount of trophies.
i was at the part in the game where madison is performing the striptease in the club and i went to check what trophy it was and it said i only had 2% of trophies…. also i cant re-sync with the server as i do not have psn (this is mobile broadband) so i will try the whole earn 1 early one and see if it re-earns them…. thanks anyway.