Thank you Rueby, I took your advice and changed my password to be more secure. I placed it here as a bug as everything else on my character looks correct, my character still has gil on hand that was not lost (around 700k) and nothing else looks out of place. I really hope there isn't any foul play and this was just some server side bug. I noticed on the lodestone there were some issues with retainers' entrusted items/gil displaying incorrectly, but as for my case my gil just isn't with my retainer at all. It could be related, that's why I made the thread here for now.

As for customer support I used the in-game support desk and pretty much wrote the same summary here with a link to this thread. I really don't know how to contact a GM directly or at least have one open an investigation to see what might have gone wrong... to be on the safe side though I'm trying not to leave any gil with my retainers until I can get more info.