You are on to something here.  I exported a 'missing tree' scene to Indigo from iClone and the meshes and texture images never make it to Indigo. 
In iClone, I deleted everything from Scene Manager - directional light, key light, shadow catcher, sky. 
With the Scene manager now empty, I loaded in a SpeedTree, which did not Display in Viewport for Render.  But it shows in Scene Manager as a Tree.
I exported to Indigo.
If you export and look in the exported folders, there is nothing there for the missing trees. 
The scene in indigo also makes no reference to a mesh or material for the missing tree, although it is listed in the Scene Manager in iClone.  

So, the components of the missing tree file never make it to indigo.  Does this mean they never made it to the iClone scene in the first place? 
Because we do see a bounding box for the tree prop.  Maybe just the mesh and materials don't convert over.  But the scene manager clearly lists them as trees in the Scene Manager, but maybe the conversion is where it gets messed up.

This tells me that it has not to do with iClone display, but the conversion of data from .itree file to an active tree prop.
-(1) Loading Stream (2) Converting Data (3) Updating User interface-

KT and Animagic -
Separated, but maybe related....when you mouse-right-click to drag an image into a scene, to be used as an image-plane, does that plane then show in the list of props in Scene Manager?
Curious, as you have working SpeedTrees, I am wondering if you would have this other 7.1 issue as well.  For some it works, and others, like myself, it does not show as a prop in Scene Manager.

Yeah, really, really weird things happen when dragging either images or video over with the right mouse button (it doesn't matter which you do).

The first time I tried it, empty scene, and I got two props to appear in the scene.  After that, no matter how many I drug over, no more appeared (they were there, they just didn't show up in the scene).  I thought it might have something to do with naming, so I renamed the first two but no luck.  Then I put a tree in (just to see) and it appeared.  I then drug one more image over on top of the tree, and IT appeared in the scene.

I tried it with a new scene and I can definitely get one to appear, but now not more than one no matter what I try.  So it's just very, very odd.  I don't think it has anything to do with your tree problem, but we do know they both use planes so I guess it's always possible (you'll know if they solve the scene appearing and trees start working for you :>).

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Alienware Aurora R16, Win 11, i9-149000KF, 3.20GHz CPU, 64GB RAM, RTX 4090 (24GB), Samsung 870 Pro 8TB, Gen3 MVNe M-2 SSD, 4TBx2, 39" Alienware Widescreen Monitor
Mike "ex-genius" Kelley

Dear Customer,
Thank you for the project link.
We had no trouble seeing the tree in the project so this would indicate the problem is a local system issue.
Looking at your dxdiag.txt we see that your graphics drivers are three years old and badly in need of updating.
Please try updating your graphics drivers and ensure you have the latest available. Please see the link below to check. This may well resolve the problem for you.

I updated the driver to the latest version to no effect.

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I have added this the feedback tracker here: https://www.reallusion.com/FeedBackTracker/Issue/Speedtrees-no-longer-showing-up

Feel free to upvote it if you experienced this issue.

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SPEEDTREE MADNESS:

Okay, I think I may be in progress to the solution...
I have now enabled a workaround.  It involves your Template folder, and reinstalling. 

From what I am doing -
if you take your current existing Template folder and rename it, say to "Template B" for example, and then reinstall iClone, creating a new Template, the default SpeedTrees work again. 
Now, because the folder will be new without your content in the folder, you will have to (a) migrate back in or (b) drag n drop from your Template B folder into the iClone scene.
BUT.... it will allow you top load in all the trees!!!!  I copied in my purchased trees from the older "Template B" to "Template", and it works!!!!

What is interesting, is that if you then now, following reinstall, flip the names back, so that iClone goes back to your older-regular Template Folder, the trees won't load.  This shows it's not the reinstall itself of the application (.exe) that fixes, but rather because it creates a new Template folder, you can reference that new one instead as "Template"...this new folder seems to be some sort of fix. 
FYI - My "older folder" was a revamped copy of iClone 6 stuff, where I added in 7 stuff, perhaps a legacy Template folder screws up stuff somehow? 
Or maybe it was size, I will see if this becomes a problem.  I am checking as I migrate content back in, but so far so good.

PS - that support reply was very generic....LOL
This is why FBT isn't the best way in all cases.  Too slow.  Fellow users like myself will try different variations and discover workarounds/potential solutions....FAST

PS - I give KT and Animagic much credit, your helpfulness lead me in the right direction...AGAIN.  :)
     

That's a good catch, Tony -- and I wonder if it explains why some folks don't have issues (maybe their folder structure is different?  Mine is -- mine is outside of the iClone installation, so much that I had to alter the registry).

Oooo -- I wonder what would have (what will?) happen if you just dragged the tree in from Windows Explorer?  Those having issues might give it a shot just to see (although it sounds as if iClone itself is doing some kind of reconcile with where the tree is stored versus maybe the authorization?  Perhaps a DRM issue?)

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Alienware Aurora R16, Win 11, i9-149000KF, 3.20GHz CPU, 64GB RAM, RTX 4090 (24GB), Samsung 870 Pro 8TB, Gen3 MVNe M-2 SSD, 4TBx2, 39" Alienware Widescreen Monitor
Mike "ex-genius" Kelley

So, I decided to do a test with dragging and dropping a video and then images in the scene, a feature that I normally don't use, and found that something strange is going on indeed.

For simplicity, I'm going to repeat this with a freshly started iClone and just images being added by right-clicking, dragging, and dropping while selecting "Plane".

I add the first image and nothing shows in the Scene Manager. I then move and do an undo, and then the image appears as plane in the Scene Manager.

I can repeat that and every time the plane is not added at first, but after moving and then undoing it appears. 

If I added a series of planes in that fashion the will not show in the Scene Manager, but once I move and undo they will all appear. They will also appear after I add something directly from the Content Manager, such as a block. 

So it looks as if the Scene Manager is not properly updated.

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SPEEDTREE vs MIX-MOVES - FIGHT!

Anyone who has missing SpeedTrees, did you also get the MixMoves pack, the one with the Communication stuff?
If you did, or even if you're not sure but you have the missing SpeedTrees, just check this out...  
Close iClone so not running.
Go into your iClone Template folder, look for the folder "MographMotion". 
In that folder, if you see a sub-folder with the name "00_Female (CC)", change the name, to something like "00_Female (CC) 1".

Now go into iClone and try your SpeedTrees, including the included default trees in the PROPS > TREE folder....tell me what happens. 
If it works, toggle the name of that folder back and forth, (back to the original "00_Female (CC)") and see if you see a repeatable and predictable pattern when you close and restart iClone, and try to then load SpeedTrees. 

I tried this, Tony, and yes, I had specific results. When I changed the CC Female folder name, the speed trees showed up in my project. When I changed it back, trees disappeared. I tried it a couple of times, consistent results. 

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I also have the same problem with the trees.
It happened this week after the upgrade from Windows10.("Fall" edition).
Sometimes the trees appear, sometimes not. 
When the trees don't appear I restart iClone, and (till now) it works.:):):)
I don't have to rename the CC female folder name.

Best Regards,
Arie