What's to say they won't sell SE alongside an SE2 that also has a more premium price like they sell 6s/7/8/soon X all at once - different generation phones still competent enough to appeal to different markets
If Apple updates the iPhone SE, I don't see them retaining the original SE in their lineup. The SE2 would be the new SE essentially. If they increase the price point, then I also have to assume they will add more capabilities and features, perhaps with an updated display, 3D Touch, etc.
On a sidenote, the iPhone SE and 6S share almost exact internals, which this is also likely the last year for the 6S to be in the iPhone lineup. And I imagine SE will follow suit behind the 6S.