Replace END with Exit Sub. The END command stops all VBA code.

Private Sub Worksheet_Change(ByVal target As Range)

    LR = Range("A65536").End(xlUp).Row

    If Not Intersect(target, Range("W2:AR" & LR)) Is Nothing _
    Or Not Intersect(target, Range("W2:W" & LR)) Is Nothing _
    Or Not Intersect(target, Range("X2:X" & LR)) Is Nothing Then
    
        If Not Intersect(target, Range("A2:T" & LR)) Is Nothing Then
        Exit Sub
        End If
    '''Or Not Intersect(target, Range("X2:X" & LR)) Is Nothing _

        frmManualEntry.Show
    
        TargetRow = target.Row
        
        Range("AU" & TargetRow).FormulaR1C1 = "@ " & Format(Now(), "hh:mm") & " by " & Environ("USERNAME")

        With Range("AS" & TargetRow)
            .Select
            .FormatConditions.Add Type:=xlExpression, Formula1:="=LEN(TRIM(AU" & TargetRow & "))=0"
           ' .FormatConditions(Range("AU" & TargetRow).FormatConditions.Count).SetFirstPriority
            With .FormatConditions(1)
                With .Interior
                    .PatternColorIndex = xlAutomatic
                    .Color = 255
                    .TintAndShade = 0
                End With
            .StopIfTrue = True
            End With
        End With
        
        
        
        MsgBox "Please enter the reason why the device was not used"
        
    End If
    
End Sub