As George says, it's just a warning to have you take a second look to make sure the return is correct before it is filed, in case you overlooked that.

You shouldn't override the FTI.  Unless you know exactly what you are doing, overriding is almost always a bad idea.  CO starts with FTI and makes various adjustments to arrive at CO taxable income.  If that return includes any non-conforming provisions, those amounts are entered as adjustments (either addition or subtractions) instead.

Question to you is whether your client's return has any non-conforming provisions due to retroactive application or decoupling.  If not, you simply need to check off the diagnostic so that you could submit the return for e-filing.