You don't need the title deeds for the HSE to do a vacate, they do it automatically, so no, they didnt need to have the title deeds then, but it would be surprising if they didnt ask where they were. Have you shown them the journal entries?
Anyway, you can get a duplicate vesting cert from the PRAI if you give them an affidavit from the legal per rep- they will tell you what they want on the affidavit. After that, probably a first registration- your new solicitor will guide you through. It's not complicated but there is a cost to it, just get a quote.