I showed up at BCN on Tuesday morning with a CRTW2 with the routing ...BCN-WAW-TXL.... I had missed the BCN-WAW the night before, and therefore asked LH to get me the fastest way to TXL.
They took the BCN-WAW segment, and gave me a BCN-MUC boarding pass, and a MUC-TXL Boarding pass with the WAW-TXL segment. They stickered that segment and wrote on it "good for MUC-TXL". No extra taxes (I suppose it would have been more expensive because of the MUC connection)and no US$ 75.
Generally they try not to reissue at airports if they can avoid it, because of the nightmare of tax recalculation and the long lines behind you.