Yes — metaflac or foobar2000 is the way to go here. The cuesheet is not part of the actual FLAC tag (which is Vorbis Comments or METADATA_BLOCK_VORBIS_COMMENT), but resides in a different block type called METADATA_BLOCK_CUESHEET. That's also the reason why it's not visible in extended tags.
I've added it to my list of future ideas for improvement.