Yes. Opportunity Partner records can be cloned using Super Clone Pro. In the clone configuration, select the partner relationship to be cloned with the opportunity.
When cloning the Partner, Salesforce requires that either the Account or Opportunity to blank. You may receive the exception message,”Opportunity: Cannot specify both Opportunity and AccountFrom”. In the configuration, try setting the field action for “Account From ID” to “Leave Empty”. The platform will then populate the “Account From ID” with the Account related to the Opportunity when the Partner is inserted.