I’ve already sent in a ticket to support, but I thought I’d post a message on the forums so others can be aware. Last night, I did a PVP attack and received some glory for which I was awarded 10 Springveil Badge Chests. I opened them for around 1600 badges and promptly redeemed them on my chosen gear path. However, the badges that I spent were not deducted from my total.
I initially thought this was just a server lag issue, so I tested it by tapping on the next prize. It actually let me claim it, so I quit Atlas and let it sit overnight hoping that it would straighten itself out. Today it still says that I have over 1600 badges and is prompting me to claim my next reward.
tl;dr, keep an eye on your badge totals, guys!