You've made this code very complicated. The main problem with it is copying and pasting cells (their formats).
Staying in the convention of your code, see how it shortened. Execution time too. :-)
Sub Painting_Dept_Identifier_1()


    Dim start_Time#, End_Time#
    Dim rngDefinedColors As Range
    
    Main_Order_No_Col = Range("Main_Order_Col").Column


    Main_Dept_Col = Range("main_line_Number").Column
    Main_Line_Column = Range("Main_Line_Number_02").Column
    Main_Header_Row = Range("planning_header_row").Row + 2


    '>>>Reading data from loading Zones
    Row_Start = Range("Loading_Zones").Row
    Column_Start = Range("Loading_Zones").Column
    Column_End = Column_Start + Range("Loading_Zones").Columns.Count - 1


    loading_Zones_row = Range("Loading_Zones").Row
    '>>> doing the loop to place the color 1st on the loading data sheet
    KL_Row_Index = Main_Header_Row


    With Application
        .Calculation = xlCalculationManual
        .ScreenUpdating = False
        .EnableEvents = False
        .DisplayAlerts = False
    End With
    
    start_Time = Timer


    'Range("Loading_Zones").ClearFormats
    
    Set rngDefinedColors = Worksheets("Lines").Range("C2:C30")


    Application.StatusBar = "Planning Calculation : Painting In Progress"


    Do While Range("Main!A1").Offset(KL_Row_Index - 1, Main_Order_No_Col - 1) <> ""


        Group_Identifier = Range("Main!A1").Offset(KL_Row_Index - 1, Main_Dept_Col - 1)
        
        Range("Main!A1").Offset(KL_Row_Index - 1, Main_Dept_Col - 1).Interior.Color = rngDefinedColors.Cells(Group_Identifier).Interior.Color
        Range("Main!A1").Offset(KL_Row_Index - 1, Main_Line_Column - 1).Interior.Color = rngDefinedColors.Cells(Group_Identifier).Interior.Color




        For Column_Index = Column_Start To Column_End


            '>>>> LOOP WHEN ZERO VALUES FOR EFFICIENT COLORING


            If Range("Main!A1").Offset(KL_Row_Index - 1, Column_Index - 1) = 0 Then


                GoTo Skip_Column


            End If




            '>>>>>>>>>>>>>>> Identify the group to color and start setting the colors on the loading zones of each _
             order and row.
            Group_Identifier = Range("Main!A1").Offset(KL_Row_Index - 1, Main_Dept_Col - 1)
            Range("Main!A1").Offset(KL_Row_Index - 1, Column_Index - 1).Interior.Color = rngDefinedColors.Cells(Group_Identifier).Interior.Color


SKIP_ROW:
Skip_Column:
        Next Column_Index
        'loading_Zones_row = loading_Zones_row + 1
        KL_Row_Index = KL_Row_Index + 1


    Loop
    '


    '    ActiveSheet.Protect DrawingObjects:=True, Contents:=True, Scenarios:=True _
         '        , AllowFormattingCells:=True, AllowFormattingColumns:=True, _
         '        AllowFormattingRows:=True, AllowDeletingRows:=True, AllowSorting:=True, _
         '        AllowFiltering:=True


    'Sheets("Master_Visual").Range("MVisual_Str") = "Y"


    End_Time = Timer
    Application.StatusBar = " Painting Completed In " & Format(End_Time - start_Time, "0.000") & "secs"
    With Application
        .Calculation = xlCalculationAutomatic
        .ScreenUpdating = True
        .EnableEvents = True
        .DisplayAlerts = True
    End With


End Sub
And that's not the optimal code yet. But maybe that's enough for you.

Artik