Get rid of whitespace on otherwise empty lines
Retina, 5 bytes

%G`\S


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A not so obvious approach rewards us with a better score :)

Explanation

G indicates this as a Grep stage, keeping only those lines where a match to the regex given (\S, matches non-space characters) can be found. If it wasn't for the starting % this would completely remove lines instead of just "emptying" them. 

The % is a modifier which applies the stage once to each line and then joins the results with newlines: in our case this means that the empty string returned by Grep for whitespace-only lines will become an empty line in the result.