It isn’t realy a Problem if you use “Save a Copy” at Endnote->File (instead of manualy copying the .enl and .data),
as the Folder- and Filenames get shortened automaticaly if you copy it by that way into a longer filepath-structure.
I only have seen corrupted files because of manualy copying.
The only Problem you could have is if you have your DB on a Networkdrive. (I had a case were the pdf wasn’t created because the filepath would have been to long).