Yes, since the incorrect method was done for 2 (or more) years in a row, that is now considered an accounting method. The way to remedy this is to file a Form 3115, not filing amended returns. Form 3115 is due by the due date of the return that the accounting method change is being made for, including the extension.
If you'd like to prepare a Form 3115, you'll need to use a Desktop version of TurboTax, and file your return by mail.
See: Application for Change in Accounting Method
