For rental property, the cost basis "for depreciation" is the LESSER of
- What you originally paid for the property or,
- The FMV of the property on the date it was placed in service
So if the property was purchased prior to 2008 and placed in service in 2008 or after, it's highly possible the FMV at the time placed in service was "in fact" lower than what you paid for it. So the CPA very well may have done it right.
Understand that you can't just arbitrarily change the cost basis of an asset. When you do that, it completely screws the depreciation history, and will make the current year depreciation wrong also.
If you are required to change the cost basis of an asset, then you have to file IRS form 3115 with your return to do that. The 3115 is included in the TTX program. But that form is not simple by any stretch. You'd be advised to seek the services of a tax professional for the 3115. Especially if your state taxes personal income.
But again, if the property was placed in service anytime after 2008, and before around 2013/14, the cost basis used "for depreciation" is probably correct.
