No, you already filed a return, the problem is that the IRS is having a hard time verifying you. You can't submit a new tax return, you need to give the IRS whatever they need to verify you. The acceptance agent is supposed to be the expert on that -- they should call the IRS as representing you, talk to the agent handling your case, and find out what they need to do to fix this. Only if the agent says to file an amended return or a different return would you do that.
I don't know the steps because this is not my area -- you hired an expert, they should fix it. If they can't, you hired the wrong expert. Find a better one and demand a refund from the first one.
