Strange the blurau/dvd is showing all sold out on Amazon JP. Wonder if they having production issues. Was never unable to preorder in the past and I have purchased every bluray.
I just ordered on CD-Japan, and there it said "11 copies of the initially supplied remaining", so it seems maybe they were only given a limited supply for pre-orders. They're surely getting more at a later date, but it might be that you'll have to wait a little after the release date for them to ship.
Do you mean the points you get when you pre-order from cdjapan? I believe they work as a minor discount when you use them for another order, but they expire after a while, so that might be why you lost yours.