I ran into the same situation with a client. If you try to apply a manual file update when you've already initiated a cloud based using the "Trigger Updates" option it will hang. I believe we restarted the mwg processes using the cli (scripts in /etc/init.d/ ). This stopped the updates and then we applied the manual file. Please note that if you restart the main mwg process it will restart all processes, causing an outage.
I'm pretty sure that's how we did it, don't have my notes in front of me here.
Thanks for Your answer, that helped. I did the same as you said but did restart the whole Gateway machine