Organize .data folder

I have about 3000 references in Endnote X4 and most have full text attachments.  The .data folder associated with the library is a mess and some of the files have very long names.  This creates exremely long paths C:\user… that cannot be indexed in sync services like dropbox or skydrive.  Is there a way to reorganize the .data folder attachments, creating short file names and paths?