Your Accountant is right. You will still need to submit your B1 (Annual Return ) with the Companies Registration Office. If it is a limited company, and unless it is the first return, you will need to have accounts/auditors report (even just basic accounts showing balance sheet, ie 100 Ordinary Shares. If you dont submit your Annual Return on time, once it is over 28 days late, it is €100 plus €3 per day outstanding after that. Costly for the sake of a €40 return.
You will also need to lodge a CT1 if the company is still Corporation Tax registered for the relevant accounts period, even if the return is Nil.
It is a relatively small excercise, but I would recommend you retain your accountant to do it for you. Sometimes people try to cut corners with "trivial exercises", such as this, which end up costing them money in the long run.