Although you may see the replicas "mixed" with the original props, the Archives does keep each piece tagged, and inventoried as such correctly. There is no mistaking a screen used piece for a replica piece with in the Archives. Lela French is a very good Archivist and made sure they were designated appropriately.
Also bare in mind that Lucas Films keeps many replicas, and uses them as decoration within the several business units at the Ranch, and former Presidio. They are not meant to fool anyone, and they are labled as such either with the manufacture name plate (eg Master Replicas) or the original manufacturers stands. Using these pieces allows the experience of Lucas Films heritage with guests/ employess while not putting at risk the original props. Also Lucas does infact rotate original props every 6 months or so in special displays throughout his properties. So you get a good mix.