Nothing will be lost, sometimes their updates just mean they take everything down and run it through an auto-republish system. When its done your mission should be exactly as you left it. But its difficult to say when it'll be done, hopefully fairly quickly.
Do we know roughly how long this will take - will I be able to edit and play my mission with friends tonight?? :/
It's a republish. Happens quite often after changes that affect the Foundry. All the missions will slowly reappear; that's already underway.
Volunteer Community Moderator for the Star Trek Online Forums. My views do not represent those of Cryptic Studios or Perfect World Entertainment. If you wish to speak to someone on the community team, file a 'forums and website' support ticket here, as we are not able to respond to PMs regarding moderation inquiries. Follow me: Twitter,Google