So, I started a NG+ today and I guess I was lucky because I didn't encounter this bug. I have all my armor. Hopefully it's sorted out soon for you.
Speaking of bugs, I actually leveled past 100 and even though more implant slots unlock they are actually not visible. You can equip implants blindly in the new slots but because they aren't visible you can't unequip them.
Has this occurred for you too?
EDIT: This has happened to others and has been raised since I wrote this.