the only mission reward that goes away is the extra reward for ep 5 which we think amy be a jem'hadar boff. The set piece rewards will stay, unless they are changing how it works, but i doubt it.
the little battery packs are not there for the replay but you can get either get a crate of them or a recipe instead.
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the little battery packs are not there for the replay but you can get either get a crate of them or a recipe instead.