File Server Migration from 2003 to 2008R2

We have a 2003 file server (NON DFS) that has an overcomplicated file structure and shares, it needs to be heavily simplified.  We have thousands of documents and entire folders that aren't used anymore.  The boss doesn't want departments deleting anything in their folders, even if it's not used for historical reasons.  To combat this, we've installed a SYNOLOGY NAS and plan to migrate our entire 2003 file server data to it and use it for historical lookups only.

I created 2 Windows 2008R2 VM's and configured them to use DFS and replication.  I've simplified the root level folders and shares for each department on these new servers.  Can I still use Microsoft's File Server Migration Tool since I going from a non DFS file server to 2 DFS replicated file servers that have completely different shares and permissions to clean this mess up moving forward?

Currently, we have to go to each department and ask what people use and migrate only that to the new servers.  This seems like such a colossal waste of time doing it this way. I don't see how the FSMT will work in this scenario but have never used it before so maybe it can be. Would someone give me some other  ideas besides visiting each department to see what they want moved?  We still plan to move everything to NAS as first and final step so it's all on that box so it can be referenced if need be.  I've done file server migrations before using ROBOCOPY but not going from 2003 non DFS to 2008r2 DFS with a new naming structure and then having to pick and choose what to migrate to new file server.

Thank you
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msandhorstAsked:
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Kylo RenConnect With a Mentor System EngineerCommented:
robocopy should be fine. just map the drives and use the mir switch along with the security switch in order to preserve your permissions
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Scott SilvaNetwork AdministratorCommented:
It might be easier to move everything to NAS, and let departments move current stuff to new shares....  That way they can deal with things like fixing obsolete shortcuts the many users insist on making to files...

That way you have everything on the NAS and don't have to worry if something gets missed... If you have enough storage for that...
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msandhorstAuthor Commented:
Robocopy is better than the only other comment made regarding letting users move things themselves cause that would never happen in the real world.  Users never do anything us IT people say they need to do, that's what GPO's are for... enforcement upon them.

We used Robocopy to grab everything and copy to the NAS then made the NAS read only for historical reasons.  There were to many file structure changes moving forward so I set permissions on the root folders in the DFS name space shares and started moving stuff manually where it needs to go.  Some users float between departments and will work out those permissions when / if they call.  So far no trouble calls yet.
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