[roann]

Usually you encode a wav file with the "Keep foreign metadata" box unchecked, i.e. if there are any non-audio parts in the wav file they will not be stored in the flac file.

From the FLAC documentation:

"FLAC is a general-purpose audio format, not just a compressed WAVE file format. There's a subtle difference. WAVE is a complicated standard; many kinds of data besides audio data can be put in it. FLAC's purpose is not to reproduce a WAVE file, including all the non-audio data that is in it, it is to losslessly compress the audio."

"Many users of the FLAC format have expressed a desire that they be able to reconstruct the original WAVE file, complete with all non-audio chunks. In their view, to be truly lossless, FLAC should be able to recreate the original file, not merely the audio waveform. While these non-audio chunks cannot be compressed using the FLAC algorithm, they can be preserved in the metadata section of the FLAC format."

"By default, flac does not store WAVE metadata ... However, if you really need to store the non-audio parts of a WAVE or AIFF file, you can use the --keep-foreign-metadata option to flac when encoding to store it in FLAC metadata, then use the option again when decoding to restore in to the decoded WAVE/AIFF file."