And why is it that some side-ops remain highlightable in white text even though I've beaten them? I can't seem to reactivate them. Seems to happen the most with extra highly-skilled experts, as if I haven't extracted all prisoners even though the game says I've completed them.
You might not be "over the level" for it to be beaten/no longer useful. That or you may not have space for the person at Mother Base despite the exaction being successful/mission complete.
I have this same problem but haven't pin-pointed the cause.