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By migrating, I assume you mean exporting / importing data between applications?
The app copy utility is a data level tool that essentially copies the database tables to the new application. All metadata, data, journals, rules, forms, grids, etc., copy over. I do not believe consolidation status changes as it would when you are importing fresh data, etc.
NOTE: The newer versions of the copy app tool do give you some additional controls over how/what is copied. For instance you can copy only specific scenarios / years, etc. This is handy if you have a specific item you want to test in a new app as you don't have to copy all data to another app.
The tool is pretty simple to use; however, always double check to Database / App information before starting to make sure you specified the source / destination correctly! :-)
After the app copies, you will need to register the app, and then I generally clone the provisioning from the production app to the new app through Shared Services.
I don't understand the question. I think what you are saying is that you can connect through Smartview and the client; however, you cannot access it through Workspace?
Generally speaking, if you copy to an new app, you still need to register the app with "shared services" and load security, etc. If you are copying into an existing application, you can get away without doing that. You register the app through workspace and the security you can load through the client by using your latest security extract from the app you copied from. (If this app is in the same environment, you can copy security/provisioning through Shared Services as well).
Disclaimer : The above is for a Class application and does not apply to EPMA apps.