I would call AY and have it all settled, just for the peace of mind. If that means cancelling flight #3, then so be it. Right now, they still know and remember what happened with their IT on 14JUN and are able to fix that easily. Then you will have those two tickets secured.

As for the third ticket, I don't know how they react to a negative balance these days. It was okay twenty years ago, by a few thousand points, actually suggested to me by CS (and they saw I had upcoming bookings and would accrue points to pay off my debt).