You will need to calculate the reduced shear capacity due to the notch and make sure it is still adequate for your loads. Take a look at section 3.4.3.2 of the NDS to check this.
A 2x12 with a half depth notch at the end will have less shear capacity than a 2x6 of the same grade. This is due to the stress concentrations that happen at notched corners as well as how dimensional lumber is graded (chances are if you rip a 2x12 down into two 2x6's the grade of the resulting 2x6's would be less than that of the original 2x12 due to locations of knots and things of that nature). You lose capacity for both the stress riser and the (lack of) grading. So, it may work, but it is not as simple as saying, "I still have the same depth I would have if this were a 2x6, and a 2x6 works"