Hello Eric,
A suggestion about locating the programs that reference a given file. In Visual COBOL for Eclipse, you can search for a string that appears in files in all open projects. This is done using the menu option Search->File (the shortcut for this is CTRL-H), then enter desired string in the "containing text" field . By default, this will search all of the open projects in the current workspace. However, you can also constrain the search to a "working set", which is a subset of projects (for this workspace) that you would have previously defined.
Since this will only search open projects, you'll need to first be sure all projects you want searched are open in Eclipse.