What you need to do is update to an AmigaOS version (and programs, like DirectoryOpus Magellan) that properly supports long file names. Just don't ask me which one, but OS3.9.2 must do since I am using it. [Note that Magellan only supports long file names if you enable it using a "secret" option.]
There is not only Opus Magellan supporting long filenames in OS 3.1 but also a little program called SRENAME (note the "S" in the beginning) and it could be find on AMINET...
Then Everblue could save the files with name truncated and then rename it with SRename...
Note that it seems to me that 3.1 does not support well long-filenames while 3.5 and 3.9 do it.
BTW... Is it sure about 3.5 supporting LFN?