@Everblue
This sounds like the programs you are using (such as Workbench & most Shell commands) do not support such long file names, therefore they get truncated.
But when (for example) copying long names, they probably just tell SFS "create a file with the same name as this file", without ever looking at the name itself. Therefore the copying program does not (usually) need to directly support long filenames.
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.]