iPad Pro keyboard stopped working in anything but internet browser

I have been experiencing this same issue. I also get the Device not Supported message. My keyboard is intermittent with all apps not just one particular app. It fails completely after several minutes of use or won't work at all when I start to use it. The space button will also start to type on its own when I start typing a few words. I find physically disconnecting it reconnecting it is the quickest way to resolve the keyboard not responding but this is not always the case. My iPad is basically my laptop so I am using it 8 hours a days at work. I have the Bluetooth on all the time because I take notes with the pencil. The pencil has not been much of any issue but I have found I need to connect it to the iPad to get it to start working but usually only after long periods of no use.

The iPad Pro is the smaller 9 inch one and less than a year old. So is the pencil and keyboard.

Hi. I'm using the Smart Keyboard for the larger iPad Pro and had some problems as well with the "accessory not supported" message and the overall unresponsiveness of the keyboard. I've had the keyboard for more than a year now and only started experiencing problems sometime last quarter 2016.

When I recently updated to iOS 10.3.1, the message disappeared but the keyboard is still intermittently responding... until I accidentally left the Bluetooth on since I started using the Pencil as an alternative.

The Smart Keyboard seems to be responding well with the Bluetooth connection on... and when I turn it off, the intermittent response returned. Maybe you can try this method out. I am unsure if Apple did anything for the keyboard interface during their last update but this is my latest experience thus far.

Hope it helps you out.