I have seen this happen. It is more prominent early game. If suffering high damage/casualties (not necessarily death). That is until DDA kicks back in. Examples that I have encountered after the Leviathan patch:
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Having trouble with Arthrons with evolved armor, the armor is removed in future encounters. Success leads to reintroduction of armor.
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A battle against Arthrons with acid grenade launchers, the launchers are removed on most Arthrons and replaced with shields in future encounters. Success and the shields are once again replaced with launchers.
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Trouble with Tritons with special abilities can lead to them being removed for future encounters.
What I have seen where this is not true, facing highly evolved enemies early on. Especially noticed in early special missions far, far away from any red mist. Where one faces fully evolved enemies including Sirens and Chirons where no Lairs could/should exist. It appears that special missions are scripted to have evolved Pandorans no matter what level the DDA is for the player.
I believe that @UnstableVoltage addressed the latter in a reply in First Mission on easy:
We’re changing the way this works in a future patch. Pandoran forces and their mutations will be more linear, though they will still have several unique upgrade paths, tied to their tech tree. The point at which they mutate and which path options are open to them will also be somewhat tied to the player’s progression.