Yes, sftp needs to be run as user Y. The main script is a start/stop process for a web based application (separate app and web servers). All the processes must be started or stopped as user X, but user Y must be used to send results to the other server detailing basically whose turn it is to run.

[app server script]
start environment (x)
start rmi (x)
sftp web (y)
wait till app continue
start scheduler (x)

[web server script]
wait till web
start web (x)
sftp app continue (y)