Search for the js_composer_theme or js_composer folder on the server
find /home/ -type d -name 'js_composer_theme'
find /home/ -type d -name 'js_composer'
Rsync from the folder you put the new files in to the output location of the commands above
rsync -vr js_composer /home/<username>/domains/<username>/public_html/wp-content/plugins/
Make sure the username is the owner of the synced update
chown -R <username>:<username> /home/<username>/domains/<domain>/public_html/wp-content/plugins/js_composer
If needed Cleanup upload dir:
find /home/ -type d -path '*/uploads/js_composer'