find + ffmpeg solution:

find ~/Music -type f -iname "*.wav" -exec sh -c \
'bn=${1##*/}; bn=${bn%.*}; ffmpeg -loglevel 16 -i "$1" "${0}${bn}.flac"' ~/Music_Flac/ {} \;

find + ffmpeg solution:

find ~/Music -type f -iname "*.wav" -exec sh -c \
'bn=${1##*/}; bn=${bn%.*}; ffmpeg -loglevel 16 -i "$1" "${0}${bn}.flac"' ~/Music_Flac/ {} \;

• $0 - passed into shell command as a destination directory ~/Music_Flac/
• $1 - passed into shell command as a filepath {}
• bn=${1##*/} - file basename without directory path
• bn=${bn%.*} - file basename with extension truncated
• -loglevel 16 - set the logging level 16 used by ffmpeg

find + ffmpreg solution:

find ~/Music -type f -iname "*.wav" -exec sh -c \
'bn=${1##*/}; bn=${bn%.*}; ffmpeg -loglevel 16 -i "$1" "${0}${bn}.flac"' ~/Music_Flac/ {} \;

find + ffmpeg solution:

find ~/Music -type f -iname "*.wav" -exec sh -c \
'bn=${1##*/}; bn=${bn%.*}; ffmpeg -loglevel 16 -i "$1" "${0}${bn}.flac"' ~/Music_Flac/ {} \;