reflac will recompress FLAC audio files in-place while preserving metadata.

# To recompress a directory of FLAC files:
reflac <path/to/directory>

# To enable maximum compression (very slow):
reflac --best <path/to/directory>

# To display filenames as they are processed:
reflac --verbose <path/to/directory>

# To recurse into subdirectories:
reflac --recursive <path/to/directory>

# To perserve file modification times:
reflac --preserve <path/to/directory>