I am trying to upgrade worklight project built using v6.1 to v6.1.0.01 and getting following error :
An internal error occurred during: "Upgrade Worklight Projects".
com.worklight.upgrader.versionGraph.VersionGraph.isKnownVersion(Ljava/lang/String;)Z
The version of studio is 6.1.0.01-20140418-0637
This could happen if your imported project is missing
either the complete org.eclipse.core.resources.prefs file in the .settings folder of your project (this is hidden file; you can see it using the Navigator view in Eclipse for example),
or if this file exists but it is missing the wl_version property.
You can fix this by creating a new project and copy over this file to your 6.1.0.0 project and then try to upgrade again to 6.1.0.01 - which you should be using 6.1.0.02 anyway by now and not 6.1.0.01.
One workaround you can do is to create a new project with the same name, etc in the Studio belonging to 6.1.0.01 and copy over your web resources and native code to the newly generated files.
You can also take a blank app in 6.1.0.0 and try to import that one to 6.1.0.01 to see whether it fails still or not. This will help in focusing the issue.