We've experienced odd behavior like this as well lately (not specific to deleting a program though). For example, when cloning a program - and defining the new program name - all references to that program should change to the new program name. Unfortunatley, it's hit-or-miss. Sometimes it changes to the new program name; other times it retains the source program name. This makes it very frustrating when we have to move that cloned program to a new workspace - and it doesn't allow you to since it's referencing a local program outside of the cloned program.