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One way to make the leaving of that secondary antagonist satisfying could be if it gives a problem for the protagonist. Now how could an antagonist leaving be a problem? Well, it is a problem if the protagonist's plans against the other antagonists required the presence of that antagonist.

Maybe the plan of the protagonist was to plot a clever scheme against the antagonists, causing the two secondary antagonists to go against the main antagonist together (not knowing that they themselves have been manipulated, of course). With the main antagonist gone and the secondary antagonists weakened by the fight, it would be much easier to win against them.

But now as the intrigue begins to work out, the one secondary antagonist gets too afraid of the main antagonist and leaves. The other antagonist, seeing that he has no chance alone, now decides to side with the main antagonist, making it look like all that already happened was solely the fault of the now gone secondary antagonist.

In other words, not only did the protagonist's original plan fail, but in addition the problem got even worse, since now the remaining antagonists are united instead of fighting each other.

In short, if the secondary antagonist leaving mid-story makes things worse for the protagonist, it is a good thing for the story.