If SecretStore is running in separate trees, you can't merge the trees without any hit to SecretStore. After the merge, only SecretStore data in the destination tree will be valid.
Before merging, delete SecretStore data from the source tree. After authenticating to the new tree, you must resave your single sign-on data.
See Merging Novell eDirectory Trees in the Novell eDirectory 8.7 Administration Guide.