I assumed that updates would not fail. If updates can fail, too, then you're pretty much stuck going through row-by-row. You could at least determine which rows should be inserts and which should be updates, in advance, by checking whether a corresponding row exists in the real table:

$to_insert_stmt = q{
SELECT * FROM scratch S
WHERE session_id = ? AND NOT EXISTS (
  SELECT 1 FROM real_data
  WHERE key_val1 = S.key_val1 AND ...
)
};
$to_update_stmt = q{
SELECT * FROM scratch S
WHERE session_id = ? AND EXISTS (
  SELECT 1 FROM real_data
  WHERE key_val1 = S.key_val1 AND ...
)
};
[download]

Then any rows that fail insert are skips, and any rows that fail update are skips, and you don't waste time trying to insert rows that should be updates.