There was a change on the format between 2.0.0 and 2.1.0.
There's an export/import tool that will be released on 2.1.2. (It's on trunk). So that won't be an issue moving forward now.
Does this mean it will happen automatically, or that we need to explicitly run the tool?
Glad to hear there is a solution.
So far we've been able to use the same data between minor versions without requiring the use of the Export/Import tool.