You may need to make these checkboxes mutually exclusive, that is, assign the same field name for each pair of checkboxes (yes and no checkboxes) but assign a different export value to each one.
For example, if I understood your intended workflow correctly, let's say that you have ten boxes ( 1 through 10 ).
I would create 10 pairs of radio buttons instead of checkbox objects which will avoid users checking both yes and no simultaneously.
Each pair would be named: rb.1, rb.2, rb.3, etc.
Since radio buttons objects are intended to be used in pairs, rb.1 group will consist oftwo radio buttons with the same name.
To make them mutually exclusive one radio button must have "yes" as the export value and the other one "no".
This way, when the user ticks rb.1 under the column of "yes" radio buttons, the rb.1 checkbox with export value of "no" will not be checked.
Is this what you are inquiring about?