I play on the Japanese server Yojimbo and our FC name is "Tenkamusou".
I've already spoken to Gm Oppiunkam about this and he has advised me to post a thread under this forum.

This happened on early this morning Japan time around 4:30 to 5:00.
I was making the final collections from our FC members, and I had 3 mail from them but did not deposit them to our FC Chest until above mentioned time.
When I did get around to deposit the sum received, I saw our sum at 2,600,000 gil for about half a second and it was gone... it went to 0 gil.
This isn't the first time we have experienced this, and the first time was not too long after we formed our FC. The amount wasn't much and everyone in our FC had access to our gil so we did not look any further in to the situation.

Our officers are currently under investigation (because we are the only ones with access to the company gil) but I fail to see any of us doing it. Further more, like I mentioned, I saw the sum for about half a second so I strongly believe it was either a bug or a hack.

Either way, I would like to say that this gil was a contribution from all of our members and we worked really hard to earn it. From the in-game message I got from SE earlier today, It really sounded like there wasn't anything you guys can do as far as reimbursement goes and this is really disappointing to me and my FC members.

We were very excited about the patch coming up and we really feel we deserve reimbursement, by you guys denying us that, it discourages playing fair and instead, doing alternative measures to earn in-game currency.

I hope this gets resolved soon and we get what we earned back. IF this does not get fixed the way I see fit, I would cancel my account for reasons obvious... and I'm sure there are others in my FC that feels the same way.
Again, WE really enjoy this game and hopefully this is not the way it's going to make me stop playing.