The only workarounds are:-
a) to individually delete each item in the current Playlist A and leave the items appended from the new PlayList B which can take a long long time if PlayList A has more than a couple of items in the List
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or b) to quit VLC and restart it with a clear and empty PlayList and repeat Quit every time you want to use a new PlayList c, D, E etc. Unsatisfactory but a lot better than Option a !
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.