Operations and cycles are checked for the deletion of their geometry.
If geometry has been deleted, this is indicated in red the Sequence window:
The checks are automatically triggered by various events. For example on entering Manufacture Mode, or if a change to the loaded solid is detected (the change being made in an external CAD package).
Note that if the automatic checks cause too much of a delay, you can suppress them by unchecking the preference Options menu ► Preferences ► Toolpaths tab ► Check for Deleted Geometry. You would then only be warned of any problems when you generate CNC code.
Note that you can also perform checks manually, on a feature-by-feature basis.