To fix this, you will have to edit the Applications.xml file within the control folder. I highly suggest opening this file up with XML Editor 2007. It makes editing an XML a snap. Once you have the XML editor open, do a ctrl+F and type in the GUID from the error screen. Click Find Next.
Once it finds the GUID, it will expand the element as shown here:
You now click on the Dependency folder associated with this GUID and delete it. Be sure to search again for the same GUID as it might be in multiple locations as shown here:
You do the same thing to delete this GUID out. I also did the same from the second error listed above.
NOTE: Make sure you backup the Applications.xml file before editing it!