If you thought your older Magic Keyboard would work with the new iPad Pro, we have some bad news. The 12.9-inch option will require the new Magic Keyboard to work. But the new Magic Keyboard will work with the third- and fourth-generation 12.9-inch iPad Pro. It seems that because the new iPad Pro is slightly thicker, this might be causing the issue. The 11-inch model doesn't have the same problem as it has the same size and weight as its predecessor.
Source: 9to5Mac