Basically, if you over ride you will not be able to e-file. It also causes other issues math-wise, as you have discovered already.
What you need to do after having gathered all your numbers including depreciation (which I get the impression you have done so already) is to report this sale in the Sale of Home (Gain or Loss) section. It's under the Personal tab in Personal Income >> Less Common Income >> Sale of Home (Gain or Loss).
