Godzilla had to go back to his home planet because he was dying of diabetes.
...no, really, that's what happened. Doesn't matter if the movie never got made, the story still got published. So it's still canon as far as I care.
Also, as should be obvious, the Godzilla in DAM is a grown up Minilla, and the Minilla in DAM is a second baby Godzilla, probably the Showa timeline's version of Junior, who, if you'll remember, hatched in 1994, just five years before DAM takes place.
And Yet Another One?