I would put them back in. On the outside

I dunno, unless glued with epoxy in time they will fall off. ( potholes, vibrations, etc ) They are in there for a good reason, as mentioned before for the metal shavings. The filter picks up some and the magnets picks up the shavings when parked. The quick fix would be purchasing a magnetic plug which are not cheap compared to the original pulg. If this were me, I would drain the oil again in a clean bucket, drop the pan and re-insert the magnets. The extra hour of doing this will help your tranny in the future.