append/link +shift D + Alt D = total confusion

Append brings a copy of of an item from another .blend but it adds geometry that slows the game engine.
Link brings a copy from another blend, without slowing the game engine but the mesh can’t be moved unless you make it a proxy.

once a mesh is brought into your .blend through one of those means, it can be copied with either shift D or Alt D.
Both create a copy, if linked it can not be edited just like the original if it is created with Alt D. A linked mesh copied with Shift D can be edited but again it slows the game engine and adds to the vert count.

Linked items can only be placed in the scene one time, any copies vanish if you save the .blend and reopen it. I linked in three trees and any copies I make vanish when the file is opened again.

so if I want to place more than one copy of each tree do I append, link, shift D copy or Alt D copy them?

also, why does the texture of the trees unlink? The material and textures are still in the file, I just have to re-apply the material each time I open the .blend?

please ignore the typing mistake in the name of this file

Shift+D makes a unique Object with unique Object Data.

Alt+D makes a unique Object, but the Object Data is shared with another object. This way you can make copies, and if you modify one, all of them change since they share the same object data.

I am not sure about your other questions about objects disappearing if you close and open the blend with linked or appended objects, or slowdown, vertex count and materials disappearing, I feel that your understanding is somewhat wrong, but I am not sure how you understand it. It would be useful if you could be more specific and post a blend for each question.

the blend I posted (although I didn’t know it) is a perfect example of what I am talking about. That scene had 6 trees and 17 boulders in it, all of them were linked to the scene and yet the are all missing from it now. the only tree that remains in the one tree that I copied using shift D, the others were copied using Alt D.

If I want to bring in an item from another .blend and can only do it using append and copying with shift D, what is link and Alt D good for?

If I link a mesh (my tree for example) how can I make a copy and move it to another point in the scene and not have the material or mesh itself vanish when I open the file again?

If I want my scene to have a lot of trees and boulders do I have to append all the trees and boulders into a single .blend file, arrange them how I want them placed and then link the final scene into my new .blend?