Why do we call it ecclesiastical separation? Some seem to think that we use this label because we are talking about separation that pertains to local churches, either in terms of their own membership or in terms of their outside fellowship. But that definition is both unhistorical and unworkable.
We call it ecclesiastical separation, not because it has to do with churches, but because it has to do with the Church. At the root of all Christian fellowship is this question: who is presumed to be within the Church? Only those who are united to Christ by His Spirit, and who are thus members of the Church Universal, are fit objects of Christian fellowship. Further, only those who have believed the true gospel are united to Christ by His Spirit.
Of course, we cannot gauge who actually possess true belief in the gospel. What we must do–what Scripture requires us to do–is to evaluate who professes faith in the true gospel. Only such individuals are presumed to be in the Church. Only such individuals are suitable subjects of Christian fellowship at any level (and Christian fellowship does have more than one level). Profession of belief in the true gospel is the minimal requirement for any Christian fellowship.
In sum, ecclesiastical separation is not fundamentally about the limitation of fellowship between churches, but about the limitation of fellowship to those within the Church.