File/share rights issue

I have an issue with share rights and user's personal directories. The directories were never setup correctly to get all or any for that matter of the correct rights. The users appear to have rights to write, create, delete files and directories in their personal drive. But I am trying to copy them to new directories where all the rights are setup properly according to our environment.
As I copy the file/directories over to the new location I am noticing that there is an issue with what I have rights to as the administrator. I notice this by the difference in the size of the directories, very considerable in some cases.

So how can I go about resetting the rights so that I can copy the files successfully.

This is all on a windows 2008r2 server in an AD enviroment
RfrytrwgssoAsked:
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rhandelsCommented:
If the users don't need to access the files anymore on the old location just make sure to first take ownership of all files within the users folders and then reset the permissions so you with your administrative account has enough permissions to copy the files.
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RfrytrwgssoAuthor Commented:
unfortunately at the moment they still need access to the directories.
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rhandelsCommented:
You could try and test with one directory, take ownership, setup permissions accordingly (so administrators full control, user change permissions) and let the user relog again. If it is just a home folder without redirection you normally won't have a problem.
If the profile folder is stored inthere and you take ownership with your admin account the profile will be corrupted along the way.
If you have a user who you can test this with give it a shot. I have no idea what's in those folders so it is quite hard to give 100% solid advice.
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compdigit44Commented:
Why not give the administrator group full access on the root the inhertient the permissoins on the subfolders

THis link may help you as well:
http://platformadmin.com/blogs/paul/2011/01/resetting-file-permissions-windows-server-2008-r2/
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rhandelsCommented:
Be sure to watch out with adding permissions on the top level if all other levels have inheritable permissions. It could be that all of the security table will be overwritten.
If case of home drives you often see that each folder has it's own permissions set, pushing security from top level down could cause major issues (could, not would).
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RfrytrwgssoAuthor Commented:
the other problem with allowing inheritable permissions is that then everyone see's everyone's home directory. I am still trying to work this as I can and haven't come up with a good solution yet as to how to do this other than go through each one. Still looking for a possible better way since that is time consuming and has issues of it's own.
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compdigit44Commented:
I understand your concerns.. How many home folders do you have ...

I did find a VBscript that will create and set permissions on home folders for users.. I know this is close but not exactly what you are looking for.

http://gallery.technet.microsoft.com/scriptcenter/02703f52-7fd6-4dfc-9ef1-0d5bdf785e4c
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