I know those objects stay in inventory if you don't leave the planet,but if you go into orbit or into sector space they will disappear.they may also have a time limit for staying in inventory,but not sure.
I don't think so. Items obtained as part of completing the mission are replaced with rewards when you turn in the mission. Rewards should never disappear. It sounds like they backed up data from a time before you obtained those perhaps, but it seems like they should be able to fix it.
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