I think he lent them to the museum and retrieved them before going to Rivendell - I am sure it says somewhere. Few Hobbits sweem to be interested in teh outside world so I guess they weren't much missed after 60 years on display. Maybe Bilbo thought he might need them for his journey.
Actually it is quite common to loan items to Museums even for a long period of time, even indefinitely, and retain ownership. If you read the cards by artefacts it will often mention that it is on loan and from whom.
