depends what is quicker for you, fixing it or starting from scratch, only you can answer that. To fix it maybe remove the duplicates with xEdit first, and then set the Master with Wrye, it sometimes works.. no guarantees
but what important here, is do you fully understand about flipping the bit the header, it is what what designates a plugin as a master, not the extension.. think of it as (sort of) a signed or unsigned integer, if ya know what that is?.. anywho it is very important the bit is flipped