Right now the Java version is still the official version. Once Red51 gets the Unity version caught up to the Java version and that replaces the Java version on the store page then the Java version will just move to the beta branch like the Unity version is now. Then you could just remove yourself from the beta branch testing and it would only load the Unity version.
So nothing you can do about it right this second, but soon-ish.
First of all copy your entire world folder and plugins folder if you use any just to be safe. Go-to the option to enable beta and set it to no beta. Once you do you should be able to uninstall Java version by right clicking on the game in library and click un install. It should only un install Java version. Worst case it un installs both. If that's the case bl unity again and drag the world's and plugins folder back into the game directory.
First of all copy your entire world folder and plugins folder if you use any just to be safe. Go-to the option to enable beta and set it to no beta. Once you do you should be able to uninstall Java version by right clicking on the game in library and click un install. It should only un install Java version. Worst case it un installs both. If that's the case bl unity again and drag the world's and plugins folder back into the game directory.
Thanks for this, I did consider that but wasn't sure what side effects there might be. I'm not too concerned about the Java version staying where it is for now, what's a little annoying is having the steam system tray icon launch the old version rather than the new.
It should have given u an option to load unity by default. If you remove the Java version it should load into unity version
Unfortunately you cannot uninstall the Java version easily... if you uninstall it through Steam, it will also remove the new version (also Steam will no longer consider the game installed, i.e you won't get updates anymore etc). This will change once the new version has officially replaced the Java version 
However, if it's mainly about Steam launching the wrong version, you could try this: rightclick on RW in your Steam library -> Properties -> General -> down at the launch options, select "New Version" in the drop down menu (by default it's set to "Ask when starting game"). Although I'm not sure if this really works in all situations 
I also have a question about this:
If the two versions switch places, i.e. Unity becomes the main game, do we still have to choose which version we want to play when we start?
And if something changes, do we have to deal with the installations again, or the paths?
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