Subtract Using GravityWP Count Plugin

Use $add_number if $sub_number is 0, else use $sub_number:

$sorting = null;
$paging = array( 'offset' => 0, 'page_size' => $page_size );
$entries = GFAPI::get_entries($formid, $search_criteria, $sorting, $paging);
$countentries = GFAPI::count_entries( $formid, $search_criteria );

if(!$sub_number) {
    $countentries_add = $add_number + $countentries;
    if ( !empty( $number_field ) ) {
        $gwp_count = $add_number;
            for ($row = 0; $row < $countentries ; $row++) {
                $gwp_count += $entries[$row][$number_field];}
                return number_format($gwp_count * $multiply, $decimals, 
    $dec_point, $thousands_sep);
    } else {
        return number_format($countentries_add * $multiply, "0", ".", 
     $thousands_sep);
        }
} else {
    $countentries_sub = $sub_number - $countentries;
    if ( !empty( $number_field ) ) {
        $gwp_count = $sub_number;
            for ($row = 0; $row < $countentries ; $row++) {
                $gwp_count -= $entries[$row][$number_field];}
                return number_format($gwp_count * $multiply, $decimals, 
    $dec_point, $thousands_sep);
    } else {
        return number_format($countentries_sub * $multiply, "0", ".", 
$thousands_sep);
        }
}

The loop will still increase the row count, you can’t count row numbers down from 0.

Or if you know $add_number is negative only if you want to subtract, you can use:

$sorting = null;
$paging = array( 'offset' => 0, 'page_size' => $page_size );
$entries = GFAPI::get_entries($formid, $search_criteria, $sorting, $paging);
$countentries = GFAPI::count_entries( $formid, $search_criteria );
$countentries_add = $add_number + $countentries;
if ( !empty( $number_field ) ) {
    $gwp_count = $add_number;
        for ($row = 0; $row < $countentries ; $row++) {
            $gwp_count += $entries[$row][$number_field];}
            if($add_number < 0) $gwp_count *= -1;
            return number_format($gwp_count * $multiply, $decimals, 
$dec_point, $thousands_sep);
} else {
    if($add_number < 0) $countentries_add *= -1;
    return number_format($countentries_add * $multiply, "0", ".", 
 $thousands_sep);
        }