Incorrect rental real estate property 20 years

I purchased property A in 2001 and entered it in TurboTax Premier. Following year 2002 I purchased another rental unit (property B) in the same building. I accidentally entered property A & B as one rental unit, then entering unit B by itself. 

I didn't notice the error until the tenant in unit A offered to buy it and I started to calculate tax ramifications. 

First 3 years I didn't take depressions on either property in the TurboTax filings. Then in 2004 what should have been property A $4,727 depreciation became $10,182 depreciation until now. Property B was OK.

I have all the TurboTax software since 2001 and pdf & tax files.

Am I allowed to amend all my returns for all those years or what should I do to correct this problem.