2nd Directory & Server Upgrades

We are using our primary (names.nsf) for internal entries but want cusnames.nsf to be a 2nd directory used for ACL purposes for external customers. My concern is that future upgrades would overwrite the custom cusnames.nsf. We have a few fields that record user registration information. It is basically 95% the names.nsf and 5% custom. If we upgrade and select “Yes” to upgrade directory, will it replace the design of our cusnames.nsf or just names.nsf? Thanks…