The "Apply All" button on the manager can make changes to a tree's materials, which are saved directly into the prefab. This can cause the change to affect copies of that tree which are found in other scenes, which is not intended and would not be what the user would expect, since each scene has its own manager, with settings that should be exclusive to that particular scene.
Values that are known to bleed across multiple scenes:
1) The HQ and LQ colors for the tree.
2) The "Billboard Quality Setting" value.
The billboard quality has been fixed in LushLOD version 0.74, affecting Unity versions 5.5 and 5.6, and should no longer bleed across multiple scenes, but has not been fixed for earlier versions of Unity.
Editing the HQ or LQ colors of a tree using the manager will still affect the tree across multiple scenes, which has not yet been fixed at all as of 0.74.
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