The simplest way that would not affect existing links (presuming you are managing the site with hidden metadata) would be to right click the file in EW's Folder List panel and copy and paste it. (Might want to paste it into a separate folder in the Folder List called "archives," for organizational purposes.) EW will automatically append "_copy(1)" to the filename, before the extension. This should have no effect on the existing file or links to it, since it still exists with the same name.
You can then edit the filename of the copy, replacing the "_copy(1)" with whatever scheme you decide to use for your archival copies—issue date, vol#_issue#, serial#, whatever... If you think about it a bit, you might be able to come up with a scheme which is naturally ASCII-sortable (e.g. vol-3_issue-4), so the archives appear in folder and other listings in chronological publication order. Just a thought...
Doing it would probably actually take less time than describing it, and you then have a consistent naming scheme that will work going forward, and can be adapted to a database schema later, if you wish. ;-)
cheers,
scott