My guess is that the rumored or previously announced departures from Boys ECNL have little to nothing to do (at least directly) with performance in league this year or recent years and more to do with the requirements in both MLS Next and Boys ECNL rules and regulations that member clubs must put their top team in their league. Boys ECNL hasn't enforced it for the past few years (which is why so many DA clubs had both), but it appears that they are trying to do so now. Indirectly, this is where performance comes in because second teams have gotten so much worse with the decline of players and the proliferation of other competition circuits and that helps explain the wide gaps in Boys ECNL this year in Socal. Any club with an MLS Next team that has been putting their second teams in Boys ECNL will likely withdraw from Boys ECNL and keep their MLS Next teams, while any club in Boys ECNL that has applied to MLS Next is doing so under the condition that it switches its top teams to MLS Next. The winner from this in Socal would be Elite Academy League, which already have the second teams of a bunch of MLS Next clubs and could get more of them.
If you check the Arizona forums, they are saying the same thing about their dual registered clubs (at least RSL-AZ) and, based on talk in other forums, it appears that at least Atlanta United, which put its developmental players in Boys ECNL just to get extra games, will be withdrawing to focus on MLS Next only.
That doesn't mean lower performing Boys ECNL clubs like LA Breakers couldn't be asked to leave, but I suspect that the league is focused now on clubs that have a structural impediment to success that breaks the member contract, since that's a more objective mechanism.