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The environment variable CALIBRE_DEVELOP_FROM must be permanently set to the folder containing the calibre source you are changing. Best is to put it in the system environment variables. You see the behavior similar to what you describe if you set it in a cmd box when you installed the source.
You must also ensure that calibre is completely shut down before changing source, including the system tray icon and the content server. Don't change source while calibre is running.
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