I don't know of any players this past Spring skipping high school soccer to participate.
ECNL supports (in theory?) participation in high school soccer, so they schedule no events in the Fall to avoid a conflict. However, as ECNL fully implements its plans you may find clubs from states that don't play Fall HS soccer could discourage HS participation rather than ECNL as an organization discouraging participation. All ECNL events ("Final Four" being the exception) and what will become league play are concentrated in the Spring/Summer months. Eliminating State Cup takes care of eliminating qualifying for Southern Regionals, Nationals, etc. as well as Premier League the next year.
The final segregation of players from USYS events will be the restriction against participation in the USYS ODP system of tryouts. High school soccer for those players playing in the Fall should be safe.