You can't fix it, other than amending the 'open' years to fix those years.

Using an incorrect Basis is not a changing in accounting method (it is a "mathematical or posting error"), so Form 3115 can't be used (some people say it can be used in the year of the sale, but I'm still not convinced of that).

The new preparer can use the correct Basis on the current return without needing to do anything special.

If the Basis was too high (and therefore too much depreciation), it is probably not a big deal.  The taxpayer has been benefiting from the 'extra' depreciation all of these years, and when the property is eventually sold, will need to pay the Unrecaptured Section 1250 Gain  on that.  Hypothetically if they have always been in the same tax bracket, they will 'break even' (or even end up better off due to being limited to 25% for the Unrecaptured Section 1250 Gain).  If the taxpayer still owns the property when she dies and it gets a step-up in Basis, then she really did good by taking too much depreciation.

If the Basis was too small (and therefore not enough depreciation), yeah, its a bummer for the taxpayer.  But the taxpayer has been signing these tax returns for the last 12 years, including 2006 that showed the Basis on her 4562.

P.S.  I just noticed that this was you, Lisa.