Spike ate them
I wondered the same thing myself; all I can figure is that they were temporarily under the care of Mr. Threehorn and his family, due to the fact that the Twin's real family (who must be a family friend of Cera's family) was unavailable at the time. The Twins were returned to their family, who possibly also reside in the Great Valley, and that family is simply never seen in a later LBT movie.
However, the serious contradiction to this is when the Gang is chasing after the twins on the way to Saurus Rock. Prior to crossing the gorge, Cera nervously says to herself: "The things I do for family..."
Meaning that, either
1) Cera, deep down, considers the twins family even if they are not.
2) They truly are family, which shoots down my theory.
If it is #2 above, then possibly they are cousins or distant relatives of Cera's family, who, like I mentioned above, were temporarily unavailable, and asked Cera's family to babysit them for awhile.
Just my 2-3 cents.