you are correct. Amending is not feasible since the error dates back to years for which no amended return can be filed. Best would be to go back to your CPA and have him/her do the work for free of filing form 3115 for both of you because apparently, they messed up as opposed to providing incorrect data. your other choices is to do it yourselves or pay a tax pro.
Explanation of the 2-year rule:
The use of an incorrect method of depreciation, which would include taking am incorrect amount, is considered the use of an incorrect accounting method. Once an incorrect accounting method has been used for two years, a Form 3115 is required to change accounting methods back to a correct method, or in this case, since the depreciation taken was incorrect, a Change in Method form must be filed. To change to the correct method, meaning to take the overlooked or correct depreciation requires the filing of the change in accounting method form, Rev. Proc. 2015-13 in most cases. (Instructions to Form 3115)
