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In fact if you use a batch file (probably modelled on the Calibre Portable.bat file in the calibre resources folder) then if you explicitly specify the config folder then Library switching is disabled so that you cannot do it by accident.
Note that have been updates to the Calibre Portable.bat file in recent weeks to slightly improve it so if you have your own batch file based on an older version it might be worth having a look at the most recent version.
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