Updated them with chdman using this script that I found:
@echo off
set mameromdir=c:\CHD
set chdmandir=d:\emm\mame
set backupdir=c:\chd2
cd %mameromdir%
for /d %%X in (%mameromdir%\*) do (
cd %%X
for %%Y in (*.chd) do (
%chdmandir%/chdman.exe -update %%X\%%Y %%X\%%Y.new
move %%X\%%Y %backupdir%\%%Y.old
ren %%X\%%Y.new %%Y
)
)
Worked like a champion!

Copy and paste the script into wordpad and save as a *.bat
Don't forget to change the directory paths.