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Are you receiving errors when you attempt to run these workflows? Is it because the executable is not in the same path or the workflow is not in the same path between DEV and PROD (or both?)?
If the engine executable is in a different path, and it is hard coded, an option would be to set the Environmental Variable PATH to the Alteryx bin directory, and then the AlteryxEngineCommand.exe could be accessed without specifying whole path to the executable. There is a helpful How to Set or Change the Path System Variable article from Java article that details this process, which will be the same for the Alteryx bin directory.
Can you please provide an example of what your workflows are doing to execute other workflows? This might help me better understand what you are trying to do and the roadblock you are facing.
Moving the path of the Alteryx Server would require a re-installation of the Server product. You would be able to migrate your MongoDB, but a re-installation would need to occur.