In my sample application I have the version in two places.
1) In the main Construct 2 screen, under the Projects panel, when you select your root project, there is a field for Version under the Properties panel. I have mine set to: 220.127.116.11
2) During export, on the BlackBerry 10 Options page (where the WebWorks install path is supplied), there is a version field which I set to 18.104.22.168.
The version in (2) is the one that I am incrementing (i.e. 22.214.171.124, 126.96.36.199, 188.8.131.52, etc.)
Does this match what you're doing in your project?