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Changing qualifier value is blocked on NotImplementedError
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This is the piece of code in question:

def changeClaimTarget(self, claim, snaktype='value', bot=True, summary=None):
  if claim.isReference or claim.isQualifier:
    raise NotImplementedError

This safeguard prevents invalid wbsetclaimvalue call. However, qualifiers should use wbsetqualifier and references should use wbsetreference.

These API modules require information that the current Pywikibot implementation cannot provide at the moment.