AFAIK, you cannot use sqlite-single-query for all kind of SQL queries.
If you are lazy and thought you could safely copy-paste your :
<?php $result = $db->sqlite-single-query($sSQL); ?>
straight from one query to the other, whatever is the query as long as it has only one line, you are wrong.
Apparently, sqlite-single-query is limited to queries that return data, that is to SELECT queries.
$sSQL = "DELETE FROM atoms WHERE ID = '8';";
$result = $db->singleQuery($sSQL);
$result = $db->query($sSQL);