Submit your Schedule C and point out that you didn't have to file the 4562 this year - the IRS said so. But the depreciation deduction will be on Schedule C anyway, if it's all that important to them.
Note that by taking the election for the safe harbor, you have expensed any qualifying items that you bought. You ought to be able to see some of these on your Schedule C deductions by looking at them closely. If they wonder where the 4562 went, you can point them to these expensed items instead.
