Unfortunately after reconfigure the IIS application pools identity and set the correct permission to the new administrators for this new AD, when I started the Commerce Server Manager it failed. Another similar behavior is to failed the snap-in.
Looking for this CSConfig options I had to run the : CSCONFIG.EXE /F to force the new configuration.
After thar the initian CS Configuration Wizard shows up.
If you had the configuration file for this enviroment you just have to load it, if not hit next.
Get the SQL Server name and instance (if you use it) for the MSCS_Admin. I my case my client changed the MSCS_Admin database name, this can cause problem if you are not alert for that. Make sure that you type the correct Admin Database name for this Commerce server environment.
Choose the correct authentication mode and hit next.
For this webservers I didn't install the Direct Mailer and CS Staging and this is all that I had to do. If you use Direct Mailer remember to configure the correct Direct Mailer user and database server because in this cenario you already have an enviroment running.
That's all, your webserver is now able to run.
