What do you mean exactly? Both models are available on store shelves, but the particular sale which you mentioned (PS2 price) was only for the 20GB model. BTW, you wrote "$400" but the retail price for the 20GB model is 49,800 yen (=$412.70) already and the sale price for the 20GB model at Don Quixote was 39,800 yen (the same as the launch price of PS2) (=$329.83) so it's $329 sale actually.
According to a price comparison site in Japan as of today
60GB (59,900 yen) (= $496.19) -> the cheapest shop = 55,369 yen (= $458.66)
http://kakaku.com/item/20504010112/
20GB (49,980 yen) (= $414.02) -> the cheapest shop = 46,000 yen (= $381.05)
http://kakaku.com/item/20504010084/
so both models get up to 4,000 yen ($33.13) price cut at certain places though major stores are still selling at the retail price.