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The NY State tax returns (all series - resident, part year resident, and non resident) begin with the Federal income/loss information. Thus the amounts reported to NY must match the amounts reported to the IRS through the Adjusted Gross Income line. In this area NY is in conformity with the IRS tax codes. Differences only appear later in the return. There is no option to treat a NY NOL differently from the Federal. Thus, if you do treat this area differently, the NYS Department of Taxation and Finance will either adjust (or as they see it, correct) the return or place it immediately for audit. In simple terms the choice you seek is not available in the way you seek it. If you chose to forgo the carry back by not filing amended NY returns they will not object but you will must then reduce any carry forward to match the Federal.
The following is extracted from the NYS form IT-203 instructions. It does specifically state that the NOL must be calculated the same way as the Federal NOL with only adjustments for Non NY items. These instructions can be read at http://www.nystax.gov/ Click the forms and instructions tab and go to the instructions for form IT-203. It is covered on page 59.
New York State net operating loss
The New York State net operating loss (NOL) to be included
in the New York State amount column of a nonresident's
Form IT‑203 must be computed in the same manner as the
corresponding federal deduction, but using only New York State
items of income, gain, loss, and deduction in the computation.
New York State modifications are not included in the
computation of the NOL or in determining the amount of loss to
be used in the carryback or carryover year.
I realize this may not be to your best interest but I can only provide the rules. Unfortunately, I do not ,make those rules.