Please give some info about how you send it over SSH, there should be some problem there (in shell escapes I think)

This should be better to send over SSH (not tested!):

ssh user@host 'perl -pi -e "s/^(ISA~.*?~.*?~.*?~.*?~.*?~.*?~.*?~)(....
+......)(....).(~.*)\$/\\1\\20\\3\\4/"'
[download]

Double escapes of \ chars become one backslash on the remote side, no need to escape tilde. Anyway, better to see your version still.