That’s a good starting point. Have you tried reencoding the files in question with the latest flac encoder? Since flac is lossless this yields no quality penalty.
You could use
flac --best --verify --padding=4096 --silent song.flac song_enc.flac
to test one song.
Or if you’d rather do it on a bigger scale you could give my python script flacr a go to do it recursively (and optionally calculate replaygain values).
flacr.py -Q for example would calculate replaygain values for all songs in the current dir + all subdirs using all threads available on the system and then reencode all .flac files with the latest encoder while showing progress bars and returning errors on the cli (once again using all available threads).
It’s my alias for flacr.py -m 32 -rp (my cpu has 16c32t).
Good luck!