The transfer parts tool allows you to move parts between libraries.
lib1 and lib2 buttons labeled '...' allow you to browse to each
library file:
After each library is selected the contents of library is displayed
in
the panel below.
Selecting a part in one of the panels allows it to be moved to the
other library using the buttons Insert or Remove. Insert moves a
part from the left library to the right library while Remove moves a
part from the right library to the left library.
When satisfied with the result hit OK to update the libraries.