[weedwacker]

You could import and then export the audio out audacity. Doing that should clean the header of any junk in wav file. You just need to set the output preferences to 24 bit audio having the header set as wav microsoft and encoding as signed 24 bit.

Though normally the flac encoder will automatically remove any substandard junk in the header when encoding. My only guess is TLH is treating warnings as errors which will abort the encoding process. The other thing you can try is the strip audio header tool in TLH using both options which should clean the junk out of the header.