What software did you use to rip the WAV files? Were they tagged then? WAV files, unfortunately, don't have a standard way of having tags as we know them in FLAC or MP3, for instance, but there are sections of the WAV files dedicated to making notes. Some programs will utilize this, but there's not a standard way of dealing with the information.
If you use the same software to make the conversion from WAV to FLAC, you might be able to preserve this information (assuming you placed the tags in the first place).
Unfortunately you've just learned first-hand one of the huge downsides of the WAV format.