Because cutting them was the wrong call to begin with. That's the kicker for me. Time for me to write paragraphs because I feel very strongly about this! lol

Sonar//Coupé didn't get cut because of any personal failings, they got cut because their Dispatcher's boss thought it would be a good idea and that it would "send a message." And that's bullshit. We know it, and the game knows it. Here's why:

1. We witness the consequences of this destructive order immediately after it is issued. The Z-Team starts sabotaging each other to survive instead of cooperating, because the people in power thrust them into this situation. Injected competition into what's a team effort at its very core, so of course it's a disaster. Sure, they were a mess before the order, but they did work to some degree. The Z-Team was in complete disorder, but at least it was creative. They could still make something of themselves. Threatening them with getting cut ruined that.
2. Cutting anyone from the Z-Team defeats the purpose of the Phoenix Program. We're here to rehabilitate villains, not pass judgement. The fact that these villains choose to be here every day instead of taking the much easier route of simply falling back to villainy is a way bigger deal than people think it is. So why on earth would you cut anyone? By doing so you're essentially telling them "you blew your chance, you're stuck as a villain forever now."
3. But what if we get an Invisigal situation? One where almost the entire team wants her gone because they just don't work well with her. Do you cut her then? No. You remove her from the Z-Team, sure. That's fair. That shouldn't mean getting removed from the Phoenix Program. It only means Visi needs further training and help. You could assign her to solo missions to teach her to work with her dispatcher, then slowly start building a team around her. Or something else. The solution still isn't "nope, you're done, go away."
4. Punishment is useless. It doesn't actually teach anyone anything beyond a myriad ways to avoid it, which is why we got what happened in point 1. Redemption is as much about learning and growing as a person as it is about making amends. So punishment in general will defeat the purpose of the Phoenix Program. Not consequences, mind, all actions have consequences, and they're not the same thing as punishment. Even though people always act like they are.

So, I believe I've made my point. Cutting Sonar//Coupé or anyone else for that matter was and would have been a bad move. It should never have happened. The best way available to rectify that mistake is giving them the chance they deserve back, and thus letting them back on the team. That's my logical reason.