I aligned my guild with the Kurzicks and have been transfering my points over as I have them, however at the moment I am doing the scavenger hunt to get the black moa mini and so had taken the befriending the Luxons quest so I could get into the turtle hatchery. Up until last night I had accumulated just over 5000 Luxon points (showing on the Luxon bar in hero tab) however after donating (what I thought were only Kurzick) faction points to my Kurzick account I found I no longer have the Luxon ones showing. Hovering the mouse over the bar it says I still have that many points on my account however they have been cleared from the unspent bar. So I now find myself having to make up those lost points which is somewhat frustrating
