When using info.magnolia.cms.util.ModuleConfigurationObservingManager (or info.magnolia.cms.util.WorkspaceObservingManager) and registering specific paths to be observed no reload (#reload() occurs when the observed node itself is deleted.

From the jcr documentation (also see javax.jcr.observation.ObservationManager#addEventListener(EventListener, int, String absPath, boolean isDeep, String[], String[], boolean)):

12.5.3.4.1 Location
[...]
If isDeep is true, only events whose associated parent node is at or below absPath will be received.

Thus only events will be triggered for direct child nodes of absPath (i.e. the observed path).

Possible solution

Register an additional observer for the parent of the actual path but for javax.jcr.observation.Event#NODE_REMOVED event types only. Additional "filtering" would have to happen too.

Please find attached a test case for info.magnolia.observation.WorkspaceEventListenerRegistrationTest that shows the limitation (see #listenToDeletionOfRegisteredPathItself()).