Projects created using the Launcher will by default be set to use the engine version that would be installed via the Launcher when you initialize your project.
If you would like to use a custom engine build then you will need to "Switch Engine Version" for your specific project. You can do this by navigating to your project directory and right-clicking on your Game.cryproject file then selecting "Switch Engine Version", choose the browse option (button with 3 dots) and find the directory your custom engine is installed to.
After doing this your engine will be registered and the project will be able to run using the engine location that you chose.
For more information:
http://docs.cryengine.com/display/CEPRO ... +a+Project
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