I think there should be an option for a guild merger, when 2 guilds choose to merge. Whether it be an item that the guild who receives the other guild needs to use. something like this:

1. Receiving Guild Buys Guild Merger Item

2. GMs from all the merging guilds group up.

3. GM from the receiving guild uses the item.

4. All GMs in the group accept or decline for their guild to merge with the receiving guild.

once this is done, all unlocked expansions from all the original guild's flagships get applied to 1 FS. same with SHs and guild bank vaults. all members and items are moved into 1 guild and 1 guild bank. same with credits. if the guild bank happens to not have enough space, the system sends the overflow to the GM in the mail.