What should a master do if he is asked to re-issue a previously-issued set of bills of lading?

Refuse, unless with the agreement of the P&I club correspondent. 

They would normally ensure that before a second set is issued, all bills of lading in the first set were returned and cancelled or destroyed (hence the requirement for the number of Bills in the set to be shown). Each bill of lading in a new set should be claused to effect that it is a replacement bill of lading, with the reason for re­issue.