If you run remote matlab-shell via tramp, see doc/remote-matlab-shell.org, and then ">> edit file", the file will not appear in the local emacs. I suspect the fix involves ssh tunneling to get emacsclient on the remote system to open files on the local system. See --tramp in https://www.gnu.org/software/emacs/manual/html_node/emacs/emacsclient-Options.html