Ordinarily, splitting the one Schedule C into two should not change the final result, unless you hit a "boundary condition".
That is, by splitting the two Schedule Cs, you cause one of them to go negative or you made some unexpected change to Schedule SE (the self-employment taxes owed on your net Schedule C income).
The first thing to check is "Is the sum of the net income of the two Schedule Cs the same as the original C? If not, why?"
Next, I would examine Schedule SE (you should now have two of them). Is the sum of the two Schedule SEs the same as the original Schedule SE? If this changes, it will reduce your sole proprietor SE tax deduction on Schedule 1 of the 1040.
The total income on the two Schedule Cs ought to be the same as the original, as well as the total expenses. Something else changed, and you'll have to run it down.
[Edited 3/19/2020 2:14 pm CDT - updated form reference]
