After some search and with the help of pokeplayer I rediscovered his message on the first page of this thread
I find this theory of yours, which places the demise of Cera's mother and her sister into the 5th movie quite interesting. Of course one might argue that it would have been to important an event to be left unmentioned (perhaps with special regard to the song Always There), but I suppose that if they can let her "disappear" without losing a word about it, they are just as capable of letting her die without pointing out that fact.
The presence of Dinah and Dana in LBT 6 might be explained that way (though not their entirely different looks from Cera), as well as the presence of a character who seemed to be Cera's mother in LBT 2 and the presence of a half-grown threehorn beside Cera's Dad in LBT 4.
However, LBT 3 doesn't fit into the scheme. If Cera's mother or any of her sisters had been around in LBT 3 I don't see how Cera's father could possibly care about her, but not about any of the others at all. I'm afraid here we cannot explain their absence with the lack of care that would have let them leave a possible death of Cera's mother in LBT 5 unmentioned.
In any case I would seem very, very plausible to think that not all of the Great Valley Dinosaurs survived the journey in LBT 5, even though they wouldn't point that fact out too clearly in the movie and stop at showing the skeleton of "some other duckbill" only.
(We may have to split this topic if this really interesting discussion is to continue)