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Because the old version of the term is left in the vocabulary and not deleted or updated with the new term.

So what I mean is that vocabulary should contain only terms that exist on at least one node.

I need this because I'm using certain vocabulary on Views as exposed filter and old terms leftovers messes it up.

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A better description of what you're looking for is "orphaned terms". There exists a module that addresses that use case, called Delete Orphaned Terms.

This is a utility module for deleting "orphaned" taxonomy terms. By default, terms with zero nodes associated with them are considered orphans, though administrators can specify the number of nodes associated with a term in order for it to be considered an orphan.

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