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@bill6 wrote:

Would I simply input the depreciation he missed out on for the last 2 years? 

It seems that my tax software has already played catchup on the missed depreciation and will average it out over the remaining life which would effectively create a double dip if I also include it as a 481(a) adjustment.

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Yes. And enter that as an "other expense" on the tax return.

Because you now are 'catching up' on the depreciation, you need to enter that amount for the "prior depreciation".  The software will then calculate the correct current year depreciation.