J'ai trouvé mac(qui est la commande shntoolutilisée pour décoder les fichiers APE) est beaucoup moins tolérant que ffmpegsi le fichier source contient des erreurs mineures.
Normalement ffmpeg, le fichier sera toujours converti complètement, mais macune erreur sera probablement générée pendant le traitement.
J'ai donc fini par écrire un script pour diviser un fichier APE en analysant le fichier CUE et en convertissant le fichier APE en fichiers FLAC séparés par des titres à l'aide de ffmpeg:
#!/usr/bin/env python2.7
import subprocess as subp
import sys
import os
from os.path import splitext, basename
import random
import glob
records = []
filename = ""
album=''
alb_artist=''
codec = 'flac'
ffmpeg_exec = 'ffmpeg'
encodingList = ('utf-8','euc-kr', 'shift-jis', 'cp936', 'big5')
filecontent = open(sys.argv[1]).read()
for enc in encodingList:
    try:
        lines = filecontent.decode(enc).split('\n')
        encoding = enc
        break
    except UnicodeDecodeError as e:
        if enc == encodingList[-1]:
            raise e
        else:
            pass
for l in lines:
    a = l.split()
    if not a:
        continue
    if a[0] == "FILE":
        filename = ' '.join(a[1:-1]).strip('\'"')
    elif a[0]=='TRACK':
        records.append({})
        records[-1]['index'] = a[1]
    elif a[0]=='TITLE':
        if len(records)>0:
            records[-1]['title'] = ' '.join(a[1:]).strip('\'"')
        else:
            album =  ' '.join(a[1:]).strip('\'"')
    elif a[0]=='INDEX' and a[1]=='01':
        timea = a[2].split(':')
        if len(timea) == 3 and int(timea[0]) >= 60:
            timea.insert(0, str(int(timea[0])/60))
            timea[1] = str(int(timea[1])%60)
        times = '{0}.{1}'.format(':'.join(timea[:-1]), timea[-1])
        records[-1]['start'] = times
    elif a[0]=='PERFORMER':
        if len(records)>1:
            records[-1]['artist'] = ' '.join(a[1:]).strip('\'"')
        else:
            alb_artist = ' '.join(a[1:]).strip('\'"')
for i, j in enumerate(records):
    try:
        j['stop'] = records[i+1]['start']
    except IndexError:
        pass
if not os.path.isfile(filename):
    tmpname = splitext(basename(sys.argv[1]))[0]+splitext(filename)[1]
    if os.path.exists(tmpname):
        filename = tmpname
        del tmpname
    else:
        for ext in ('.ape', '.flac', '.wav', '.mp3'):
            tmpname = splitext(filename)[0] + ext
            if os.path.exists(tmpname):
                filename = tmpname
                break
if not os.path.isfile(filename):
    raise IOError("Can't not find file: {0}".format(filename))
fstat = os.stat(filename)
atime = fstat.st_atime
mtime = fstat.st_mtime
records[-1]['stop'] = '99:59:59'
if filename.lower().endswith('.flac'):
    tmpfile = filename
else:
    tmpfile = splitext(filename)[0] + str(random.randint(10000,90000)) + '.flac'
try:
    if filename != tmpfile:
        ret = subp.call([ffmpeg_exec, '-hide_banner', '-y', '-i', filename, 
            '-c:a', codec,'-compression_level','12','-f','flac',tmpfile])
        if ret != 0:
            raise SystemExit('Converting failed.')
    for i in records:
        output = i['index'] +' - '+ i['title']+'.flac'
        commandline = [ffmpeg_exec, '-hide_banner', 
        '-y', '-i', tmpfile,
        '-c', 'copy', 
        '-ss', i['start'], '-to', i['stop'],
        '-metadata', u'title={0}'.format(i['title']), 
        '-metadata', u'artist={0}'.format(i.get('artist', '')),
        '-metadata', u'performer={0}'.format(i.get('artist', '')),
        '-metadata', u'album={0}'.format(album), 
        '-metadata', 'track={0}/{1}'.format(i['index'], len(records)), 
        '-metadata', u'album_artist={0}'.format(alb_artist), 
        '-metadata', u'composer={0}'.format(alb_artist), 
        '-metadata', 'encoder=Meow', 
        '-write_id3v1', '1', 
        output]
        ret = subp.call(commandline)
        if ret == 0:
            os.utime(output, (atime, mtime))
finally:
    if os.path.isfile(tmpfile):
        os.remove(tmpfile)