In Plato layout, when you set the Die Shape to an Ink that is intended for the die line contours, why does art become clipped?
You may have a double compound path situation (due to a degenerated stroked path) as shown in the left Plato Station below. In this case, there is a double or nearly duplicate set of contours inserted for some other purpose than to be the final Die Shape. Given that these contours have the same Separation name, both sets are considered when this ink is selected for the 'Die Shape' in Grid layout.
As an alternative (shown on the right), give the other set of contours an appropriate spot Ink name so as to differentiate from the Die Shape Ink.
In the sample on the right, the interior set of contours are intended to indicate a safety margin. This Ink is given the name Safety and when Cut Ink is chosen for Die Shape, the result clips the bleed to the value chosen, and all other interior artwork remains visible.