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IIRC, the Supervision Army works the same way as the Zentradi Army, only they're meaned to fight the Protoculture.
Original Protoculture citizens are all long dead, the SA remains are vats-created Zentradi.
As for the brainwashing, IIRC it is said in Macross 7 that after a certain time under its effect, it became permanent.
They were no civilians in the SA, just soldiers to destroy the Protoculture commanded by the Protodeviln, and then acting according to the directives of the former masters, like the Zentradi.
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