Editing embedded components in Eagle
Open the layout in Eagle and run the user language program exp-project-lbr.ulp. This can be done by clicking the ULP button and finding the file in the directory or simply by typing run exp-project-lbr.ulp into the command bar. This ULP comes with Eagle and the default selections work well so this should be all you need to do.

Run this by first clicking the Collect Data button then the Create Library button. Save the extracted library wherever you like. You can now edit the parts in this library.

Make sure this new library is in your library search path in the command window.

Finally, use the replace command to first select the edited part and select the old part in the layout to swap it out.