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I have a list of more then 9000 items, the user want me to move items from that list to a folder. As administrator I created a view that shows the 9000 items (in pages of 250 items).

However if I use the "Site Content and Structure" and go to that list, it shows the default view and I see some folders there (but not the items that are not yet in a folder) and if a switch to my own (just created) view, it does show me the items in a "normal screen" it does'nt show me the items in the "Site Content and Structure" and now I cannot move the items ..please advice

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You can use powershell script to move items from that list to folder (example):

1.Get list from web

[Microsoft.SharePoint.SPSite] $Site = New-Object Microsoft.SharePoint.SPSite($WebURL);             
[Microsoft.SharePoint.SPWeb] $Web = $Site.OpenWeb();             
[Microsoft.SharePoint.SPList] $List = $Web.Lists[$ListDisplayName];  

2.Then create a query to get all files without folders and move it all to new folder

$FolderToMoveTo = $List.RootFolder.Url + "/" + $FolderName;            
$ItemMoveCount=0;                         
$Query = New-Object Microsoft.SharePoint.SPQuery;             
$Query.Folder = $list.RootFolder;     
$camlQuery = "<Where></Where>"
$Query.Query = $camlQuery         
$Query.RowLimit = 9000; #limit query because of large folder    
$List.GetItems($Query) | Where {$_.ContentType.Name -ne "Folder"} |              
foreach-object {                     
 #Line below will simply output to console and demonstrates another .NET call             
 [System.String]::format("Moving Item {0} with ID {1}...",$_.Name, $_.ID.ToString());             
 $Web.GetFile($_.Url).MoveTo([System.String]::format({0}/{1}",$FolderToMoveTo,$_.Name));            
 write-host "Success...";             
 $ItemMoveCount++;             
};             

3.Dispose web and site

#dispose:             
$Web.Dispose();             
$Site.Dispose(); 
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We had the same problem. In SP 2010, using "manage content and structure" doesn't show you any subfolders when your list is over 5000 items. The list/library has a plus sign next to it but it disappears when you click on it, instead of expanding.

To fix the problem (without re-creating the list or using PS):

-set up a "Daily Time Window for Large Queries" in Central Admin > Manage Web Applications > your web app > General Settings > Resource Throttling

-during the daily window, add an index on your list on the Content Type field

-that's it. Now SP can query your large list for folders, so you can use Manage Site Content & Structure to move items to subfolders, no matter how many items are in the list

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