First of all. -eyebleed-
Second, this is all like. Two huge sentences, so I don't understand your question. xD
What is it that's disappearing?
If you mean that your objects aren't working, its probably because you have them in a default object group, such as MyTrees, MyRocks, etc.
They need their own.
And I don't know what the 'wombat meshes?' is all about. xD