Is there a way to delete one of several checkboxes from a pdf form without the leftover checkboxes automatically renumbering themselves?
I believe you're using the same name for each checkbox, right?!
If so, each checkbox has an index number which represents its position relative to the other copies in the XML tree and when you add, delete or reorder the copies the index will always be recreated because thats the way how XML works.
There is no way to stop Designer from doing this, I'm afraid.