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Sorry about all this. What version of Unity are you using?

In the lower quality settings, the cross fade is more obvious because the fades by breaking the billboard / high quality mesh into dithered pixel-y patterns. But in the higher quality settings, it uses a post-processing shader to do the fade. I assume you are using one of the lower qualtiy settings... because you say you are seeing pixels.

When I originally designed LushLOD, I tested it with the option to fade the trees fully once the transition got triggered. I didn't think it looked as good. Because when you are standing still, it's much easier to tell that the trees are "changing shape", than when you are moving. When your whole camera is moving, that movement kind of helps to hide the fact that the trees are changing. So when I would stand still and a few of the trees continued to change shape, while the other trees didn't, I thought it looked way more obvious. But I was also using rather rounded looking trees where the pixels didn't stand out very much, so partially transitioned trees didn't leave obvious pixels on my screen.

I include the full source with my package. Each tree has a script attached to it, which controls the value of the transition as a float value. If you think it would look better to transition all the way, it wouldn't be too hard for you to get your hands on that float value and simply add a timer of some sort, to transition it fully once it starts to transition. If I remember correctly, I made the transition code slightly more complicated than I should have, so I apologize if you find it messy. ;p

Sorry but I doubt it... I imagine I have those features disabled.

ApplyAll is meant to apply any changes that you made to the settings in the manager. So if you change some slider bar or change the LOD value, you have to click applyall to apply the change. Once you've click ApplyAll, you shouldn't need to click it again unless you change something in the manager. So then, once you've clicked applyall, and then you change nothing in the manger, but you move a tree, it should have no affect to click applyall again? Because there's no changes to apply? I would think that if you've clicked applyall once, then from that point on if you move a tree, you would still need to click recalculate parents each time you move a tree. 

Basically, the ApplyAll button applies changes made in the manager, to the trees. 

But recalculate parents button, associates trees with each other, based on their proximity to each other. And that's why if you move a tree, it's proximity to other trees around it changes, which is why you need to recalculate parents. My trees do not all claculate their distance to the camera, as that would be very expensive to do for a large number of trees in the scene. So instead, I designed this parenting system. The "parents" calculate their distance to the camera, and if the camera gets close to a parent, then the parent tells all the nearby trees around it, to start their LOD transitionins as needed. This is why if you move a tree, it may need to be assigned to a different "parent", or else it will not receive the message to start its LOD transition when it is supposed to. That's what the recalculate parents button is for, and that's why you need to click it each time you move or add new trees to the scene. I can't remember if the apply all button actually calls recalculate parents for you, but I don't think it does, so I'm not sure why clicking it fixed anything, but if it did then that's great. :)

The function that needs to be called is the "recalculate parents" function. There should be a button for it in the LushLOD Trees Manager window. Or, you can manually call that function from your code. The function is located in the _LushLODTreesManager.cs file. Any time you add any new trees, and any time you move any trees around, that function needs to be called again.

Since the time of my last comment 2 weeks ago, I've posted a major update to LushLOD Trees. It's now version 0.8, and there are new features, more controls over the way shadows are rendered in the leaves, and better handling of ambient light in the trees. But it will only install LushLOD version 0.8 if you have Unity 2018.1 or higher.

I will continue to fix bugs in older versions though, so if you still have problems with running the trees on Unity 2017, let me know. But just wanted to let you know that there's quite a nice update waiting for you when you do decide to upgrade to Unity 2018.1. :)

I just wanted to drop in to say that I'm currently uploading LushLOD version 0.8, which will be the first update for Unity 2018.1+. In this update, I don't think the issue with the wind zones has been addressed. But the problem with the flickering *may* be fixed. I do know that significant improvements and changes were made to the way the trees handle lighting, including ambient occlusion. If the flickering had anything to do with ambient occlusion, there's a chance it may be fixed. The update should appear on the asset store within the next few days, once it is approved.

I loaded the project into 2017.3 and loaded the demo scene, and it didn't give me any error about the alder not having a mesh renderer. Could it be possible that you damaged the alder file? Maybe reinstalling the project file for the alder tree would solve that problem.

As for the light baking, that's an easy fix, I'll fix that error message and post an update soon with that change.

Sorry for the late reply. Updating to 2018 won't fix this, I'll need to fix this on my end. I'll let you know once I've done the fix.