I've been seeing a number of discussions in different places where it is being said that the Java version is going away later this year. In a pinned post in the RW Steam Discussions this is said about that and I am including what is said about compatibility between the 2 versions.
"What happens to the Java version?
Once the new version is ready, we will move the current Java version to a separate beta branch in Steam, so it will still be available (as well as the according server files). It's our intention to provide at least bugfixes for the Java version.
What about old worlds? Will they still be compatible?
We're currently implementing a completely new world generation algorithm from scratch, unfortunately it will not be compatible with old worlds (but of course you can still play old worlds with the Java version).
However, it's our goal to keep blueprints compatible with the new version, so you can create at least blueprints of your important buildings and use them in the new version.
It will take some time until the new version is ready, so there is definitely no need to stop playing now."