In principle, these file handles are a good thing. It is file handles which allows for the WPS's superior features of program objects and shadows working even after the files they point to have been moved to a different location. Basically, this works because program objects and shadows never store the physical path of an object, but only an object handle.
For details about object handles, see "About Object Handles."
Note that xfix mostly deals with file-system handles. To fix abstract objects,
you might use Henk Kelder's CHECKINI program.