Without a sample workbook with the latest macros, it's hard to say

Here's a snippet that "looks OK" to me

I think it's easier to 'reset' to a visible configuration each time and then apply the specifics. So I like to unhide all rows and hide the checkboxes and the depending on the choices, hide N/A rows and show the checkboxes

One the checkboxes are made visible, they stay visible until they get hidden and by always starting with a known configuration, I find it easier to manage

    Application.EnableEvents = False
    Unprotect Password:="dlm"
    
    Shapes("RFR20").Visible = False
    Shapes("RFR40").Visible = False
    Shapes("RFR40HQ").Visible = False
    Shapes("Priority20").Visible = False
    Shapes("Priority40").Visible = False
    Shapes("Priority40HQ").Visible = False
     
    Rows("1:86").Hidden = False
    
     
    Select Case rC3.Value & "#" & rC4.Value
        Case "Air" & "#" & "Warsaw to New York"
            Range("A6").EntireRow.Hidden = True
            Range("A12:A21").EntireRow.Hidden = True
            Range("A23:A25").EntireRow.Hidden = True
            
        Case "Air" & "#" & "Warsaw to Los Angeles"
            Range("A6").EntireRow.Hidden = True
            Range("A12:A21").EntireRow.Hidden = True
            Range("A23:A25").EntireRow.Hidden = True
                    
        Case "Air" & "#" & "Malpensa to New York"
            Range("A6").EntireRow.Hidden = True
            Range("A8").EntireRow.Hidden = True
            Range("A12:A21").EntireRow.Hidden = True
            Range("A23:A25").EntireRow.Hidden = True