I'm one of the GM's of Dark Hour and the same thing happened to us, but it was when we first started saving up gil. We lost 1.3m. May not seem like a lot, but it really put a stop to our saving up gil for a while.
Someone joined the FC, got promoted up to the second rank, and withdrew all of our gil. He then left and deleted his character.
We were forced to change the ranks so that no one but the leader can withdraw gil, and no one but the leader can change rank settings.
Our first response from SE was that this was basically our fault for trusting any member with promotion privilages.
Our second response said that this bug should be reported on the forums. But either way, we were told that there would be no way for us to get our gil back.
Our third and final attempt, I was told that it would be brought to the attention of the developers and I would get a follow up later on. Nothing was ever done or followed up on.
I hate to compare this... but in WoW once we had an issue where someone stole gold from our guild, and within an hour we had it all back and every item too. I was hacked and had my gold stolen from my personal character and it was replaced within 20 minutes.
This is not something that is "working as intended" and it is not the fault of any FC. This is an issue with the hierarchy system in this game that lets members promote above their own rank. This is SE's fault and them not replacing the gil stolen due to this ovesight is complete bs.
/rant