LDAP Query Failed (using old domain)

We did a domain rename last month and I thought everything was fine.  I've now noticed that AD isn't syncing with SEP.

Do I have to delete the OU structure in SEP and then re-import to get it to be correct or is there another method?

I saw a post earlier about having to delete the OU structure and then reimport because the structure is using the old domain.  Will I have to reapply policies to each OU when I re-add?