Hi Rob,
I'm not an expert at all, but maybe I'll be able to help. At least, I can try.
Your WAV file contains, next to the audio portion, some additional information used by certain software, which is called metadata.
When you encode your wav file to flac, you have an option to remove this metadata. I guess that's because it'll allow the flac file to become a bit smaller.
AFAIK, TLH's default setting is that it removes this metadata. If you want to preserve it, so the metadata information gets taken into the flac file, check the option 'Keep foreign metadata' in the 'Encode wav files' window in TLH.
Hope that helps,
Eric
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