Some good news. It seems to only be 47 files in the CHD set that were corrupt, and so you can just delete those and rejoin the new torrent at 93% to download the fixed files. The list of corrupted files to delete before joining the new torrent are:

a51site4\a51site4-2_0.chd
azumanga\gdl-0018.chd
batlgr2\bg2_201j.chd
bdrdown\gdl-0023a.chd
bhead2k\beachhead2000_5-27-2003.chd
bhead2k2\beachhead2002_5-27-2003.chd
bhead2k3\beachhead2003desertwar_5-27-2003.chd
bhead2ka\beachhead2000_9-16-2001.chd
bntyhunt\bntyhunt.chd
chocomk\gdl-0014a.chd
eztouch\szz_cf.chd
gvrxpsup\vr_xp_system_6-11-2002.chd
gvrxpsys\globalvr_xp_system.chd
hyperath\hyperath.chd
hyperv2\hyperv2_pqi_6-12-02.chd
hyperv2a\hyperv2_pqi_9-30-01.chd
ikaruga\gdl-0010.chd
inidv3cy\gds-0039b.chd
initdv3e\gds-0033.chd
jojo\cap-jjk-3.chd
jojoba\cap-jjm-1.chd
karous\gdl-0040.chd
kdeadeye\kdeadeye.chd
mj3\gdx-0017f.chd
nagano98\nagano98.chd
nfsug\nfsug1_1-disc1.chd
nfsug\nfsug1_1-disc2.chd
ngdup23e\gds-0023e.chd
pbball96\pbball96.chd
psyvar2\gdl-0024.chd
puyofev\gds-0031.chd
pwrshovl\pwrshovl.chd
senko\gdl-0030a.chd
shikgam2\gdl-0021.chd
simpbowl\simpbowl.chd
starseek\gdl-0005.chd
susume\gv027j1.chd
tokimosh\755jaa01.chd
tokimosp\756jab01.chd
trgheart\gdl-0036a.chd
trizeal\gdl-0026.chd
undefeat\gdl-0035.chd
vf4tuned\gds-0036f.chd
voyager\voyager.chd
weddingr\weddingr.chd
wswe\c18jaa03.chd
wswe2k3\c27jaa03.chd