:) Ignoring all the issues with your code with short-circuit

sub section_del {
    return $Section_tblw->clear;
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looks like Tk::Table is not deleting checkboxes

so I replace that with  return my_clear( $Section_tblw ); and one or three dd-Dumper-ings later, its an off-by-one error in clear

sub my_clear {
    my $self = shift;
    my $rows = $self->cget( -rows );
    my $cols = $self->cget( -columns );
## 1st row is labels
    foreach my $r ( 1 .. $rows ) {
#~         foreach my $c ( 1 .. $cols ) {
## 1st column is 1st column
        foreach my $c ( 0 .. $cols ) {
            my $old = $self->get( $r, $c );
            next unless $old;
            $self->LostSlave( $old );
            $old->destroy;
        }
    }
    $self->_init;
    $self->QueueLayout( Tk::Table::_SlaveSize() );
} ## end sub my_clear
[download]

I imagine the OBO error migt stem because at one point the first column in each row might have been a counter (nth row) ...