In the Reconcile tab, for your missing stock, I’m sure there are two options: ‘Never sent them to FBA’ and ‘Definitely sent to FBA; please check’. For the excess stock it’s similar: ‘Sent too many’ or ‘Definitely didn’t send too many; please check’.
It would only make sense to tell the truth here. For your missing stock you’d need to make sure you get Amazon to check the bin for them by marking the ‘please check’ option. I’ve heard stories where Amazon have miscalculated shipment contents - a discrepancy of 8 is quite high though for one product (maybe the associate was a bit tired). I’ve only ever had one discrepancy and this was resolved (found in the wrong bin) before the Reconcile tab ever opened up.
For the excess of stock, you should of course choose ‘please check’ as well. As you rightly pointed out, what are Amazon going to do when a customer orders your phantom stock? The only thing they could do is cancel the customer’s orders (which would be annoying for you as the customer might leave a negative feedback, and you’d have to complain to Amazon to get it removed), or send a piece of air to them if they’re really stupid (which, again, might result in negative feedback and FBA fees to send a cardboard box).
Once you’ve selected the ‘please check’ boxes, I’m not sure exactly how it works but I think you can just click a button and the FC will be notified to check on your stock. If they can’t resolve your discrepancies, I think that’s when you have to get Seller Support involved if you’re that bothered about getting it sorted.
And no, you certainly shouldn’t get any sort of ‘black mark’ on your account (if you do I would be very surprised). In fact, there’s a whole report on problems detected with your shipments: https://sellercentral.amazon.co.uk/gp/fba/inbound-performance/index.html/ref=ag_fbaipm_cont_xx, and Inbound Performance comes up nowhere in the Seller Performance pages. Don’t worry about it.
Oh, and before you do anything - make sure you definitely did send the missing 8