Not sure with the new system, but the old system, there are audits/counts of the cash in the machine. They have to deplete the cash and re-fill it a few times a week. I'm pretty sure it's still the same now.
I'd go in the branch where the ATM is located and talk to the manager politely. Ask if he/she can go into the machine and check if your money got stuck somewhere that's not noticeable. Just explain to him/her the situation and be as nice as possible. After all, your money is technically not even there.
They used to keep logs of the over/under cash count too. I used to work there and found loose bills all over the place.
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