Hi Song,
If it is possible to revert back to an empty database with SQL Management (i.e. prior to enabling the Enterprise GDB) this would be preferable.
Otherwise if this is not possible (as was our case) after disabling the UN topology; we needed to delete the UN dataset (containing the domain featureclasses and UN topology entity); and the nonspatialobject tables for each domain using the delete data management tool. Then we had to iterate over all the domains in a python script to remove the numerous UN domains (all out domains where UN related in our EGDB). Only then could we call stageUN and applyAP tools again to repopulate using a modified data model.
Note we have only used this technique to prototype upgrading to UN v5 in a staging environment were this this process worked for us, but if you are getting errors from the tools I would think esri tech support may need to assist you.