According to this article: http://support.apple.com/kb/TS3180?viewlocale=en_US I am required to remove the ldap binding of my second Mac OS X Lion server before I set it up as a replica server. I initially set the server up as a replica, or so I thought, and created file shares (it refers to the first server's ACL) before I realized it was never promoted as a replica server. So as of now it's running and shares files with correct ACL permissions but if the Master goes down all the file shares seize up. I want to set it up as a replica so this is not an issue; however, I don't want to lose the file shares and their permissions as I remove the binding and restart the server-- apparently I must remove the ldap binding to the OD Master (also a Mac OS X Lion server) before setting it up as a replica.
Removing bindings or destroying a directory won't do anything to your fileshares. However, you need to be careful that you keep UIDs and UUIDs consistent.