How to replace all the aliases

Something like this should work pretty fast

Put this tag on a page:

[[!FixAlias]]

Create a snippet called FixAlias with this code, then visit the page with the tag:

/* FixAlias snippet */
$docs = $modx->getCollection('modResource');
$output = "";
foreach ($docs as $doc) {
    $oldAlias = $doc->get('alias');
    if (strpos($oldAlias, ',') !== false) {
        $newAlias = str_replace(',', "", $oldAlias);
        $doc->set('alias', $newAlias);
        $output .= '<br>Changed ' . $oldAlias . ' to ' . $newAlias;
        $doc->save();
    }
}

return $output;

For a dry-run, you can just comment out the $doc->save() line, like this:

// $doc->save();

After a real run, refresh the URIs as suggested by halftrainedharry.