Hi there,

If you decide excluding the gross income from one Schedule C is appropriate, you can go to "Other Information" on screen 16, and check the box "Exclude from SE retirement plan deduction". 

You can also press F1 while on that input field to open help, which has more detail on the code sections and publications you may want to dig into regarding this decision. The diagnostic is just to alert you this option is available, if appropriate. 

- Rebecca