Creating a folder must have created a problem with the file json. Don't worry, the files haven't been deleted, it's just a file that lists the tree structure that is impacted.
You can correct the problem by looking for the file in GameClient/Data/assets.json
Then paste it into _Projects/Demo/Data/
This will replace the broken file. Or you can create a new project and delete the others. Or do a project reset (second tab of the Project Manager, I admit I haven't tested that one yet)
For trees, they would not have a parent and child link ? If they are merged as a single mesh it should not be possible to select the trunk on one side and the foliage on the other. I don't use "blender", so I don't really know. If you use trees that I made, this does not do this.
I'm going to look tomorrow at the tree you sent by email. You can also look at your tree with the inspector who will tell you a little more about your mesh.
Here is a new patch which corrects the creation of folders in Media :
The patch does not affect everything contained in _Projects/. So you need to replace the broken assets.json file as explained. Or create a new one.