This is one of the few times I'd recommend you meet with a good CPA. You will have depreciation recapture issues, and perhaps cost basis issues.
I concur with Drifterrider on this one. If you reported a different amount of depreciation for certain years, best case is that you could amend some return(s), worst case is that you will have to file form 3115 and/or do depreciation recapture. If you look at the 3115 instructions, the IRS estimates an insane amount of time to prepare this form.
Form Recordkeeping Learning about the law Preparing and sending
or the form the form to the IRS
3115 38 hr., 29 min. 19 hr., 54 min. 23 hr., 48 min.
Sch. A 3 hr., 21 min. 1 hr., 51 min. 3 hr., 11 min.
Sch. B 1 hr., 25 min. 30 min. 33 min.
Sch. C 5 hr., 1 min. 45 min. 2 hr., 4 min.
Sch. D 27 hr., 30 min. 1 hr., 59 min. 2 hr., 31 min.
Sch. E 3 hr., 49 min. 1 hr., 59 min. 2 hr., 8 min.
This link to Publication 946 should give you more information.
https://www.irs.gov/publications/p946/ch01.html#en_US_2013_publink1000107384