Hi. I'm not 100% sure what you're asking, but I have a suspicion I know what's going on.
I think you are changing the value list (the choices of check/tick boxes that display for the field).
You have a field, "Response," formatted on the layout as a check box and using the value list, "Response Options."
You enter data into the Response field for various records.
Understand that with check boxes, every item you check adds a return-delimited value to the Response field (in the order checked, btw). Furthermore—most important—understand that if you change the values in "Response Options" value list, you are not changing the existing entries in the Response field. Therefore, if your original value list is
and you later remove "Blue" from the list, that entry remains in the field for any record where it was previously selected.
If this is what you are actually doing, it would explain why your export contains data you don't anticipate.
If you turn off the checkboxes in FileMaker, you can see what data are actually there.
A checkbox set is just an interface convention for data entry. In the background, the values are stored as a return-delimited list. It's just a text field, with the values separated by carriage returns.
I suspect there are values still in the list, but there's no difference in the data between the different views. It's all the same field underneath.