Any project created in the older version needs to be updated to the new version.
You may need to make a selection at update time between Android or Crosswalk setting. The old build settings are saved. But for what purpose? if every time you need to address the Android or Crosswalk choice.
Can you keep multiple versions of Intel XDK at the same time?
You should check the Crosswalk option unless your app is very, very simple. See this Intel XDK doc page > https://software.intel.com/en-us/xdk/docs/why-use-crosswalk-for-android-builds <