I don't see a box that says "not all is income," which you put in quotes. Do you mean the box that says "This amount in box 1a is too high or includes some personal transactions"?
If that's the box you are referring to, I see your point. The wording is poor. It seems like the check box really means "show me the field where I can enter an amount to be excluded." Unchecking the box hides the field on the screen, but does not remove the entry. That seems to be a design decision, not an error. The remedy is to simply delete the amount or change it to zero before you uncheck the box. That works for me. You do not have to "remove the form and re-enter it completely," as you stated in your original question.
You also said "When I remove the entry (zero it out), the totals do not change." I am not seeing that. If I delete the excluded amount or change it to zero the totals recalculate as soon as I press Tab or click somewhere else on the screen.
(You can test this with one 1099-K in business income. Having two 1099-Ks doesn't seem to make any difference.)
I doubt that TurboTax would consider this a software defect. I don't think they will do anything about it unless there are a lot of complaints. I have not seen any other complaints about it.
