I don't know if Anno had even decided what he would end up doing with them when he inserted many of the mysterious elements in the new films. I will note, though, that there is a precedent for "sequel theory" that might have influenced Anno. Go Nagai's Violence Jack was revealed in its final chapters to have been a sequel to Devilman. In Violence Jack, it turns out that, after its destruction, the world was recreated by the fallen angel Ryo Asuka for the sake of trying to resurrect Akira Fudo, whom he had fallen in love with. However, the recreation was not entirely successful.
Without question, Anno is familiar with Violence Jack (according to the Japanese wikipedia, in Schizo, Anno mentions the Slum King as one source of inspiration for the design of the Evangelions). In addition, some Eva fans have noted parallels between Ryo Asuka and Kaworu Nagisa (including Halicat and Synapsid on EGF). Kaworu's appearances in NME especially seem reminiscent of both Ryo Asuka and the storyline of Violence Jack. However, that doesn't mean Anno deliberately intended to follow the approach of Violence Jack somehow; because many of Anno's influences emerge unconsciously, and in particular the influence of Devilman on the original NGE emerged this way, it may be that the mysterious elements involving Kaworu are a kind of unconscious echo of Violence Jack, and not directly related to a conscious intention. But, if there is some sort of "loop" involved in NME, possibly Violence Jack was a source of inspiration for it.