They can't. The current system cannot differentiate between different versions of the same item. It can either accept and return an item with 1 specific augment, or one without any. Because the augmented version is the final version, they chose to store that one. Given enough time, and possibly some adjustments to the augments in light of the new 2hrs, all armor pieces will be augmented. That YOU (as in the reader of this post) will not do that, is irrelevant.
And reworking the system is not possible due to the severity of the change needed and the temporary nature of the discomfort.


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