@andrew42 Some of these theories are interesting but until the show itself establishes any of this, I just don't buy it at the moment. Also, even though I compare the Ben 10 reboot to the previous shows (mostly the original show), I would really rely on what was established in any of the previous shows to explain certain elements in the reboot...because this is a full continuity reboot. Everything that the previous shows established doesn't apply to this show. They could (and very much often have) use elements from the previous shows but this show is still separate from the previous shows. I also agree with @Oldtaku_dd. With the way that this show is structured as, I doubt that the Ben 10 reboot is going to get as deep as you guys try to discuss it as.
Taking it as face value, Ben's DNA got deleted (or it glitch out or something) from the Omnitrix and somehow Vilgax was able to restore Ben's DNA. That's it. That's all I got to say about that very aspect of Omni-Tricked so far and I doubt that the show is going to go any deeper with that. If Ben's DNA really did get deleted from the Omnitrix, then it doesn't make sense as to how Vilgax restored it since that Ben's DNA wouldn't even be in the Omnitrix anymore...because it got deleted.