I've had that happen before in older versions of Domino Designer. Sometimes closing Designer and restarting solves the problem.
The .xsp-config file can be found in Package Explorer and holds the information to display the custom control in the Controls Palette as well as any custom properties. It can be opened directly from there and opens in the XML editor. In a worst case scenario, you can always delete the properties or other XML entities, then paste back in once it's working again (or add the properties back in using the Properties pane). The .xsp file (the underlying Custom Control) can also be opened in the XML Editor by right-clicking in the Package Explorer and selecting Open With and choosing the XML Editor.
Because of the underlying Eclipse functionality, you can delete an XML-based component - XPage, Custom Control, xsp-config - create a new entry with the same name, and use Compare With > Local History to see previous versions. Local History is stored based on the text file name. So you have a (short-term) back, even without source control.