Board Thread:Questions and Answers/@comment-181.53.142.129-20151013232257/@comment-4807396-20151023050438

Yeah, all it does is prevent Mission 45 from triggering. You can keep Quiet around, but you'll won't be able to get a couple of Key Items (and thus get 100% completion) until you do Mission 45. Just having the emblem part isn't enough, though, just so we're clear; you do have to have it on your emblem to get the effect.

The confusion might come from the fact that A Quiet Exit doesn't trigger until your bond with Quiet is maxed. As for the suppressed Guilty Butterfly, you're good as long as Quiet's bond stays above 80%. Just don't get her seriously injured and don't attack her yourself.