There is an issue in current versions of Carbide Motion where they cut the perimeter of a pocket first — I suspect that that is part of what is happening, and that your edit to the file changed it away from doing so.
If you have a further difficulty, immediately send the .c2d file, step-by-step notes on how you are securing your stock and setting zero relative to it and managing all tool changes, and a photo showing an attempt at cutting still in place on the machine to support@carbide3d.com and we will do our best to assist.