HG bought up the remaining Animeigo sets from Animeigo since their license had expired, and Tommy said that the standard practice is that they (Animeigo) were going to destroy the remaining stock.
So, in short, YES, they're re-releasing the Animeigo set, under a different box design. According to what Tommy said, they're releasing all 9 discs at once since they (RT.COM) are out of the original 9 disc sets. I don't think they are selling the smaller 3 disc sets.
Also, you will still be able to get them from Animeigo for a limited time.
Thanks for clearing that up .