Who would argue that the letters are not written to what Christ considered genuine churches? What he could commend in them he did, what he couldn't, he sought to amend. The assumption seems to have been that the members of these churches were part of the kingdom, but that their status as such was in danger. Those considered presently part of the body of Christ by Christ could end up not retaining that status if repentance was not forthcoming. Their status could be considered Once-Saved-Not-Necessarily-Saved-Thereafter, it seems to me.
If Adam and Eve, pristinely, immaculately made by God, can fall from belief into estrangement with God and sin, then anyone with less wholeness (i.e. all the rest of us, even the born-again) can fall too. If those born-again would fall, they'd be just as lost as Adam and Eve and the host born to them afterwards. If humans as perfect as they can be this side of eternity fell from a state that was deemed "good" in God's sight into unbelief and separation from God, then why would anyone in Christ think he or she could not?