I ended up building in a check for ‘~’ as the first character, around line 296 in classes/Output.php :

foreach($files as $f){
$title = esc_html($f->file_name);
$firstletter = substr($title, 0, 1);
if($firstletter!=’~’){
$file_items[$i++] = (object)array(
‘id’=>sprintf($file_id_format, $f->file_id),
‘text’=>$filesel?(‘file_id,str_replace(‘\”,’\\\”,htmlspecialchars(stripslashes($f->file_display_name)))).'”>’.esc_html($f->GetTitle(24)).’ <span style=”font-size:75%;vertical-align:top;”>’.esc_html($f->file_name).'</span>’):$f->GenTpl2(‘filebrowser’, false),
‘classes’=>$filesel?’file’:null,
‘hasChildren’=>false
);
}}