trophies work the same in cfw/mfw as on ofw and can be uploaded to psn as long as you can connect to psn.as of right now rebug rex 4.21.01 can connect and use everything on psn (except the psn-ps2 games,im not sure if this is a model specific issue only though, but the rebug team is working on it)the only way to loose trophies is to format the hard drive without uploading them to psn,the ps3 will automatically sync your trophies with psn when ever you look at them when connected to psn
the only way of hacking that will delete your trophies is if your flashing the system to a lower firmware but ive never done that so im not sure on it
if your ps3 is already below 3.55ofw you should not have this issue and your trophies should still be the same after installing cfw
as for your wording im guessing you might have meant you want to unlock trophies for games without unlocking them in game, there are homebrew apps that do this but im don't support its use
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and eating thrifty maid noodles because of it......seriously!?! off brand noodles.....ouch i got burned by tech support.....ouch........