Since the accounting change for the error from impermissible to permissble method has gone on for more than the second year, amending would also be incorrect. The proper method is to file form 3115, code 7 if the assets have not yet been disposed of, and the 481 adjustment that will be negative should be shown on Sch E. Doing so will put the prior years' adjustment into the category of a passive activity loss (as if) the depreciation and PALs had been calculated correctly all along, and then take the current year's depreciation on the proper line of Sch E.
If the assets have already been disposed of, use code 107 on the form 3115 that basically eliminates the allowed or allowable "penalty" of never having taken the deduction but having to use the reduced basis at sale.