It gets a bit complicated.
Honda CBR500R is CBR400R in Japan, they're identical except the 400R is sleeved down 500R
Ninja 650 is Ninja 400 in Japan, they're identical except the Ninja 400 is sleeved down Ninja 650.
Now they have Ninja 400 in USA/Canada
If they sell 2018 Ninja 400 in Japan, things will get complicated because they already have Ninja 400 (sleeved down Ninja 650)
Not as complicated as you think. The old 400R will simply be replaced with the new 400. There's no reason to continue producing the sleeved down 650, that was only done to meet license requirements and the new Ninja 400 meets them as it sits.
That doesn't mean there's any certainty they'll bring the Ninja 250 stateside, it's just a suggestion as it would seem to make sense and allow them to bump the price of the new Ninja 400 up to $6k.
The new 250 makes as much power as the old 300, so it could be a new lower priced entry level bike at $4-4.5k, but there's no suggestion from Kawi that that is going to happen here.