I don't know why if this option was turned off at time of import you would still see the two files, unless somehow file naming had come to differ between the pair or they were being imported within separate batches.
FYI in case unaware: no immediate effect would be seen anyway, for already imported images, from turning this option on or off.
Its setting only controls LrC's behaviour towards newly-imported image pairs. Either they come in as a raw and a JPG, or as a Raw+JPG. Then that is what they will remain.