Hi. I didn't realize your site was so big.
Yes, that would be a very tedious process. Anyway, not tested much but perhaps try the following.
Make a file called cleanup_dashes.php with the below content, stick it in the PhpDig admin directory, and call it from the browser. Once done, run the other cleans to shore up the engine (remove orphan keywords, etcetera).
PHP Code:
<?php
echo "<html><body>";
$count = 0;
$relative_script_path = '..';
include "$relative_script_path/includes/config.php";
include "$relative_script_path/libs/auth.php";
include "$relative_script_path/admin/robot_functions.php";
$query = mysql_query("SELECT spider_id FROM ".PHPDIG_DB_PREFIX."spider WHERE file = '';");
while ($row = mysql_fetch_array($query)) {
mysql_query("DELETE FROM ".PHPDIG_DB_PREFIX."engine WHERE spider_id=".$row['spider_id'].";");
mysql_query("DELETE FROM ".PHPDIG_DB_PREFIX."spider WHERE spider_id=".$row['spider_id'].";");
phpdigDelText($relative_script_path,$spider_id);
$count++;
echo $count . "<br>\n";
}
echo "<br>Done. <a href=\"index.php\" target=\"_top\">[Back]</a> to admin interface.";
echo "</body></html>";
?>
Remember to remove any "word" wrapping in the above code.