Ame, it turns out no one ever found out, was deep in the professional Media Production in the USA. The setup she has makes a lot more business sense if you're moving on in life but want to keep a door open for special occasions. Gura and Fauna made the most absolutely sense to fully graduate. Mumei seemed more like a fork in the road situation for her and it's just better to end it rather than let it hang over. Same with Aqua and Shion, but you can see that Chloe went the affiliate status because she found a primary career she wanted to peruse (as well as bring up an Indie Vtuber so she can stream occasionally).So far in HoloEN, the cases for graduation have been specific enough to just not warrant it. Fauna being able to return once in a blue moon wouldn't fix what I assume was her getting sick of the byzantinian management bureaucracy, it wouldn't have cured Mumei's health issues, and the last thing Gura wants is now all eyes on her any time she appears as an affiliated guest for an event. Ame didn't want to fully cut ties with Hololive for whatever reason; there was enough to incentivize her to appear every so often.
I doubt we'll ever get any information on Gura's discussions with management, but it's hard to probably describe how much they'd have likely done to keep her around. Everyone forgets Ayame exists for 10 months a year. Cover can make situations work.