Hi Sam,
When you say CoralNet's output, do you mean its automatic annotations?
If so, note that if you originally uploaded the point locations using CPCe files, the order of the points should be preserved. So if you opened that same CPCe file in the CPCe software, then the nth point listed by CPCe would be the same as the nth point listed if you open the image in CoralNet's annotation tool.
Not sure if that answers your question, so let me know if you wanted to know something else.
Using the Image Actions -> Delete Annotations Only function will indeed leave the point locations untouched.