The instructions for the Bonus Depreciation Add Back clearly states "Figure the Net Income (or loss) that would have been included in federal adjusted gross income had the bonus depreciation method not been used.  Then, enter the difference, which may be a positive or negative amount."  If they intended you to just add back the bonus depreciation amount taken, less current year depreciation on the bonus amount, they wouldn't tell you to figure the net income or loss that would have been included in federal AGI.  Lacerte does it the same way.

Additionally, page 39 of the Indiana Audit Manual states:

BONUS DEPRECIATION ADDBACK/DEDUCTION REQUIREMENTS FOR AN INDIVIDUAL Add or subtract the amount necessary to make the adjusted gross income of any customer that owns property for which bonus depreciation was allowed in the current taxable year or in an earlier taxable year equal to the amount of adjusted gross income that would have been computed had an election not been made under Section 168(k) of the Internal Revenue Code to apply bonus depreciation to the property in the year that it was placed in service. IC 6-3-1-3.5(a)15

Which appears to agree with instructions and ProSeries and Lacerte's calculations.  If ProSeries and Lacerte are both doing it, I tend to lean towards they know what they're doing when it also agrees with the instructions and Audit Manual.  I would also consider the same with basis loss limitations.