I'm GM of <Champions of Valhalla>, Republic side, Shadowlands server. One of my officers commented earlier in this discussion but I did want to touch bases with everyone as well and I would like to express my own frustrations with bioware for not handling this in a timely manner.
As with many other guilds we spent months saving credits to be able to enjoy the guild flagship the day that it was released. Since it's release, we have spent countless hours on flashpoints, operations, crafting and battling commanders to be able to unlock rooms (6 unlocks so far) and to collect the decorations to where we could truly call this place our haven. So for us not to be able to use it or have limited functionality only helps to anger our members.
Bioware, please fix this soon.
As for those who are also suffering from the guild flagship problems, here's what we've discovered:
1.) In order to travel to the guild flagship or to use the flagship transport option, someone must be on the guildship.
2.) If the person on the guild flagship logs in after you, you must log out to the character screen and log back in. Upon login, you will be able to access the guildship in the SH menu and to use flagship transport.
3.) When the guild flagship reappears, completion score is automatically 0%. Going into edit mode and making any edits (even simply picking up and putting down the same object) will put the completion to the correct percentage.
4.) Without anyone aboard the flagship, it disappears completely from the SH menu. Public listings will show "offline" but not indicate the name of the ship or any information.
5.) If you are on the guildship and are teleported for a warzone, you will be teleported back to the guildship afterward. Flashpoints are the same as long as you remember to select the exit area option which allows you to go back to your original location.
I would highly recommend that everyone try to park at least one infrequently used alt on their flagship in the case someone needs immediate access to it. This shouldn't be as much of a concern for a larger guild, but for a smaller guild... this could be your only way of saving it from disappearing completely.