Endnote creates the references.enl and a set of folders in references.DATA. both are needed for the library tp function properly and both reference.enl and references.DATA should be in the same folder (i.e. references.enl should not be IN the .DATA folder).
BTW, You can rescue the references.enl from the references. DATA folder, if the enl library is lost. create a file named references. DATA (or whatever the library-name.DATA is) and then open it. It shoudl magically reconstruct itself.
but 12K is pretty small.