When heating the copper in the final step, the bright copper color changes to a dull brown. will the percent recovery be too high, too low, or unaffected ?

The percent recovery will be low.

when Copper is an element in the periodic table Cu with atomic number equal to 29.

This is a metallic element that its color change from bright reddish to dull brown when it reacts with O2 and gives copper oxide.

 Also, this has very high electrical and thermal conductivity. 

 This metal, when freshly exposed is a reddish-orange color. and here above, it is described that copper has already reacted with oxygen, as its color has been changed to dull brown.

This means that the percent recovery of the metal will be low when a portion of it has already reacted and lost in the reaction.