As with all trophies lost during that glitch – your best bet is to contact the devs and explain what happened. Sometimes they can unlock the trophy remotely for you. If that fails you just might have to straight up earn it again. Hopefully you can do so with having to delete the data on your ps3 – I would ask about that too were I you.
Yup, Luckily I wasn't affected by the mini Y2K but from the problems I've read about you will need to get on to NaughtyDog. E-mail might work but if you get them on the phone, there is less chance you will be ignored, (not that by beloved NaughtyDog would do that anyways *coughs shakily*)