Managed to find a reddit page ( https://www.reddit.com/r/PSO2/comments/hiecxm/star_gems_disappearing/ ) that is discussing this exact issue. I would recommend supporting that post as much as possible if you are having this issue, as well as submitting a ticket to customer support.
The long and short of it is that both AC and SG are set to expire 1 year after purchase in Japan to avoid taxation of both corporations and people due to weird laws that Japan has. If you buy any additional AC and SG, the timer resets. However, this does not apply to earned SG as it does not have value under those laws. Though this still doesn't explain why SG is disappearing from NA users - the game hasn't even been out for a year in NA yet.