Since sqlite is just a simple file-level locking DB, I'm pretty shocked they don't have an option to let the indexes be stored in separate files for all kinds of obvious and beneficial reasons, like the fact that you can easily exclude them from backups if they were, and you can make them "rebuild" just by deleting them. Probably their reason for keeping all internal has to do with being sure indexes are never out of sync, but that could just as easily be accomplished with hashing algos.