Per the linked mailing list post there’s no dust but there is a back channel through which you can be notified:
> SQLite
comes with instrumentation (specifically the SQLITE_STMTSTATUS_AUTOINDEX
verb for sqlite3_stmt_status() - http://www.sqlite.org/c3ref/stmt_status.html) that can be used to detect when automatic indices are used and alert the developer through a back channel to this fact so that she can fix the problem with an appropriate
CREATE INDEX. In other words, SQLite provides you with the tools to help you detect and eliminate the use of automatic indices.
The transient indexes will be created in a separate, temporary file. They will be erased on a commit, rollback, or crash recovery. They will not persist.