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What do you mean by 'recognise all my libraries when I start Calibre?' -- calibre can only access one library at a time, and IIRC you cannot force portable to start with specific library.
The Find Duplicates plugin has a 'Find library duplicates' that will find duplicates in another library, but it won't auto delete from either library.
Depending on what your doing you might find the CalibreSpy plugin useful, it provides a concurrent Read Only GUI that can be used on multiple libraries.
BR
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