Not really ... we do have a character replacement function but it is only available for FTP and other Internet protocols (it's on the Internet dialog). Maybe you could switch to using FTP for the last files which need the replacement.
I think the only filename length limitation is that a filename can't be longer than 250 characters or so. But the total path with folder and filenames can be 32767 characters long. If there are problems, maybe it would be worthwhile to run the Windows version of the software on the receiving end.