You can ONLY fix it by filing Form 3115 (and I suggest a good tax professional for this year).
Because you did not claim depreciation for the first two years, that has set the "Accounting Method". That means two things (1) you are not allowed to amend to claim depreciation; you must file Form 3115 in order to 'catch up' on the depreciation and (2) you can't start claiming depreciation now unless you file Form 3115.
