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maj3091 - Copy libraries B & C into the Library A Portable folder so you have something like this
Now start calibre portable and use the Library->Switch/Create to 'register' libraries B & C
Once your happy, and you've backed up the 3 library portable install (in my example that would be D:\_Sandpit\Calibre Portable A) then you can probably delete the original Library B and C installs.
BR