Yamato has always had odd internal continuity. In the second original film (w/ the Comet Empire), Kodai and Yuki drove the Yamato into Zordar's dreadnaught destroying it, and killing themselves in the process. This differentiates from series 2 where Trelena basically wipes out Zordar with her energy, allowing them to live. The other movies (w/ the Dark Nebula Empire and Dinguil) continue to be made along with Series III (Bolar Wars), with Kodai and Yuki still alive. The live-action ends with Kodai doing the same thing to wipe out the Gamilas, but if they ever want to do a sequel, they could probably have some wiggle room, as I don't think they showed anything but a distant explosion.
So, long and short of it, they play fast and loose with Yamato's continuity. As with many such reboots, I would consider this to be in a different universe/time line. I just hope it doesn't contain thinly-veiled political commentary like the more recent "Yamato Resurrection" had. I was starting to get a little irritated with that, but I suspect that was Nishizaki's influence at the time.