I need to delete rows from an SQLite table where their row IDs do not exist in another table. The SELECT statement returns the correct rows:
SELECT * FROM ca
Since you going down the route of subquery, might as well get rid of the join altogether and simplify the query:
DELETE FROM cache WHERE id NOT IN (SELECT id from main);
SQLite apparently doesn't support joins with the delete statement, as you can see on the Syntax diagrams. You should however be able to use a subquery to delete them.
ie.
DELETE FROM cache WHERE id IN
(SELECT cache.id FROM cache LEFT JOIN main ON cache.id=main.id WHERE main.id IS NULL);
(Not tested)