I do believe that cuetools would handle the transcoding. I know for a fact that it'll copy over the metadata - I've used it to transcode a mysteriously semi-broken flac file that would work on some decoders and not others, and it has an excellent validation system (accuraterip or CTDB) that checks disks against a database of hashes for tracks and disks.
The only 'manual' step would be to delete the source files once you are done.
The UI takes a little getting used to, and its a little esoteric, but its should do what you need.