Take a look on subinacl.exe that is part of resource kit
Replace a single user:
subinacl.exe /subdirectories c:\path\to\folder /replace=olddomain\olduser
=newdomain
\newuser
Replace domain:
subinacl.exe /subdirectories c:\path\to\folder /changedomain=olddomain=ne
wdomain
changedomain action can be used with a mapping file if you only want to affect specific users. The trailing "=both" is used if it shall both first check for a match in the mapping file and also use the replace of having same username in old and new domain.
subinacl.exe /subdirectories c:\path\to\folder /changedomain=olddomain=ne
wdomain=ma
ppingfile=
both
subinacl.exe is downloadable from MS:
http://www.microsoft.com/downloads/details.aspx?FamilyID=E8BA3E56-D8FE-4A91-93CF-ED6985E3927B&displaylang=en