Uh, no. It doesn't change anything about the 12.9" Pro, or the fact that a 9.7" will still exist.
Except this is exactly what Apple is planning to do with the next gen iPhone and they have great desire and great need to evolve their most popular entry in the iPad lineup at this time. It is without argument that Apple needs a major technology bump in the iPad department to reinvigorate interest. A larger, nearly edge to edge display, possibly with a Touch Bar section replacing the physical Home Button, all inside the known footprint of the most successful iPad...is a huge head turner for the product.
Nope. The lineup soon will be:
12.9" Pro
10.5" Pro
9.7" Air 3
7.9" Mini 4