@[LoD]Wise never heard of this issue. did you tame them?

More info pls. Tamed? Wild? Bred? If tamed or bred, maybe you forgot to feed them? Babies need to be manually fed until they are juvenile and can be fed through trough ;)

My mod does nothing with despawning creatures.

I have had the same issue, however, I have found that its not the baby mod that is causing it. When you are rendering your map, especially on The Center, if the dinos render before the land does, they have a chance to fall through the map. For some reason, baby Quetz's (or any animal for that matter) don't map very well with the terrain. I have also had the problem with a few other animals. I find sitting there and waiting for them to grow from egg to adult greatly reduces the chance of it happening. If you are an admin on your server, use the fly and ghost commands to glitch through the main terrain to the base model, which is usually water, sometimes you can glitch them back up if you are lucky.

@vixen thank you for the clarification!

@Vixen
Thx for the info. I had similar issue before with dinos falling through ceilings, but good to know it could happen with land as well.
For the ceiling issue, for me it often worked, if I just whistled my dinos to follow me so they glitched back to the proper floor.
Maybe this could help other players without admin rights for their owned dinos.