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To clarify, you didn't actually lose the armour, it's just that overheat damage ignores it. If you overheated and then got shot, it wouldn't necessarily have gone internal.
If you overheat in the middle of a battle (try to avoid this, but occasionally worth it to get that extra damage to kill a mech) you'll see you still have all your armor available. The summary screen shows it that way just to inform you that there's internal structure damage that needs to be repaired.
Think of it this way... your internal structure needs to be repaired... in order to do that, they need to strip the armor from the damaged areas first, repair the internals, and put the armor back. Thus "armor stripped from overheating".