Usando merge..output para obtener el mapeo entre source.id y target.id

En mi opinión, este es un gran uso de MERGE y salida. Lo he usado en varios escenarios y no he experimentado ninguna rareza hasta la fecha. Por ejemplo, aquí hay una configuración de prueba que clona una carpeta y todos los archivos (identidad) dentro de ella en una carpeta recién creada (guid).

DECLARE @FolderIndex TABLE (FolderId UNIQUEIDENTIFIER PRIMARY KEY, FolderName varchar(25));
INSERT INTO @FolderIndex 
    (FolderId, FolderName)
    VALUES(newid(), 'OriginalFolder');

DECLARE @FileIndex TABLE (FileId int identity(1,1) PRIMARY KEY, FileName varchar(10));
INSERT INTO @FileIndex 
    (FileName)
    VALUES('test.txt');

DECLARE @FileFolder TABLE (FolderId UNIQUEIDENTIFIER, FileId int, PRIMARY KEY(FolderId, FileId));
INSERT INTO @FileFolder 
    (FolderId, FileId)
    SELECT  FolderId, 
            FileId
    FROM    @FolderIndex
    CROSS JOIN  @FileIndex;  -- just to illustrate

DECLARE @sFolder TABLE (FromFolderId UNIQUEIDENTIFIER, ToFolderId UNIQUEIDENTIFIER);
DECLARE @sFile TABLE (FromFileId int, ToFileId int);

-- copy Folder Structure
MERGE @FolderIndex fi
USING   (   SELECT  1 [Dummy],
                    FolderId, 
                    FolderName
            FROM    @FolderIndex [fi]
            WHERE   FolderName = 'OriginalFolder'
        ) d ON  d.Dummy = 0
WHEN NOT MATCHED 
THEN INSERT 
    (FolderId, FolderName)
    VALUES (newid(), 'copy_'+FolderName)
OUTPUT  d.FolderId,
        INSERTED.FolderId
INTO    @sFolder (FromFolderId, toFolderId);

-- copy File structure
MERGE   @FileIndex fi
USING   (   SELECT  1 [Dummy],
                    fi.FileId, 
                    fi.[FileName]
            FROM    @FileIndex fi
            INNER
            JOIN    @FileFolder fm ON 
                    fi.FileId = fm.FileId
            INNER
            JOIN    @FolderIndex fo ON 
                    fm.FolderId = fo.FolderId
            WHERE   fo.FolderName = 'OriginalFolder'
        ) d ON  d.Dummy = 0
WHEN NOT MATCHED 
THEN INSERT ([FileName])
    VALUES ([FileName])
OUTPUT  d.FileId,
        INSERTED.FileId
INTO    @sFile (FromFileId, toFileId);

-- link new files to Folders
INSERT INTO @FileFolder (FileId, FolderId)
    SELECT  sfi.toFileId, sfo.toFolderId
    FROM    @FileFolder fm
    INNER
    JOIN    @sFile sfi ON  
            fm.FileId = sfi.FromFileId
    INNER
    JOIN    @sFolder sfo ON 
            fm.FolderId = sfo.FromFolderId
-- return    
SELECT  * 
FROM    @FileIndex fi 
JOIN    @FileFolder ff ON  
        fi.FileId = ff.FileId 
JOIN    @FolderIndex fo ON  
        ff.FolderId = fo.FolderId