Found an easier way to reproduce the bug the error:
1 - Create a new project and add CreateMaterialInNewFolder.cs file.
2 - Use the new menu Reproduce/Crash
3 - See the same "guid is unitialised" error popup.

It's crashing in GUIDPersistentManagerV2::PathIDToFileIdentifierInternal during the AssetDatabase.StopAssetEditing call with the new material having an invalid guid.

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Original description:

I downloaded some speedtree assets from the asset store, moved the speedtree object to a separate folder to reorganise them and then wanted to regenerate the materials.
I get a crash every time i try to regenerate the material.

Repro steps:
1.download this project
2. navigate to Mushrroms/Mushrooms and click on any of the speedtree objects
3. click "regenerate speedtree materials"
4. there is dialogue that says: "GUID is unintialised"
5. Unity crashes afterwards

Cannot reproduce in Unity Editor 2019.1.0b11, 2019.2.0a4
Reproduced in Unity Editor 2019.2.0a5, 2019.2.0a11

Only reproduced when using Asset Database V2

From the Editor.log:

guid is uninitialized
UnityEditor.SpeedTreeImporter:GenerateMaterials()
UnityEditor.SpeedTreeImporterInspector:GenerateMaterials() (at C:\buildslave\unity\build\Editor\Mono\ImportSettings\SpeedTreeImporterInspector.cs:154)
UnityEditor.SpeedTreeImporterInspector:OnApplyRevertGUI() (at C:\buildslave\unity\build\Editor\Mono\ImportSettings\SpeedTreeImporterInspector.cs:115)
UnityEditor.Experimental.AssetImporters.AssetImporterEditor:ApplyRevertGUI() (at C:\buildslave\unity\build\Modules\AssetPipelineEditor\ImportSettings\AssetImporterEditor.cs:615)
UnityEditor.AssetImporterTabbedEditor:OnInspectorGUI() (at C:\buildslave\unity\build\Modules\AssetPipelineEditor\ImportSettings\AssetImporterTabbedEditor.cs:100)
UnityEditor.UIElements.<CreateIMGUIInspectorFromEditor>c__AnonStorey1:<>m__0() (at C:\buildslave\unity\build\Editor\Mono\Inspector\InspectorElement.cs:479)
UnityEngine.UIElements.IMGUIContainer:DoOnGUI(Event, Matrix4x4, Rect, Boolean, Rect) (at C:\buildslave\unity\build\Modules\UIElements\IMGUIContainer.cs:281)
UnityEngine.UIElements.IMGUIContainer:HandleIMGUIEvent(Event, Matrix4x4, Rect) (at C:\buildslave\unity\build\Modules\UIElements\IMGUIContainer.cs:483)
UnityEngine.UIElements.IMGUIContainer:HandleIMGUIEvent(Event) (at C:\buildslave\unity\build\Modules\UIElements\IMGUIContainer.cs:466)
UnityEngine.UIElements.IMGUIContainer:HandleEvent(EventBase) (at C:\buildslave\unity\build\Modules\UIElements\IMGUIContainer.cs:447)
UnityEngine.UIElements.MouseCaptureDispatchingStrategy:DispatchEvent(EventBase, IPanel) (at C:\buildslave\unity\build\Modules\UIElements\Events\MouseCaptureDispatchingStrategy.cs:93)
UnityEngine.UIElements.EventDispatcher:ProcessEvent(EventBase, IPanel) (at C:\buildslave\unity\build\Modules\UIElements\EventDispatcher.cs:280)
UnityEngine.UIElements.EventDispatcher:Dispatch(EventBase, IPanel, DispatchMode) (at C:\buildslave\unity\build\Modules\UIElements\EventDispatcher.cs:156)
UnityEngine.UIElements.BaseVisualElementPanel:SendEvent(EventBase, DispatchMode) (at C:\buildslave\unity\build\Modules\UIElements\Panel.cs:188)
UnityEngine.UIElements.UIElementsUtility:DoDispatch(BaseVisualElementPanel) (at C:\buildslave\unity\build\Modules\UIElements\UIElementsUtility.cs:255)
UnityEngine.UIElements.UIElementsUtility:ProcessEvent(Int32, IntPtr) (at C:\buildslave\unity\build\Modules\UIElements\UIElementsUtility.cs:78)
UnityEngine.GUIUtility:ProcessEvent(Int32, IntPtr) (at C:\buildslave\unity\build\Modules\IMGUI\GUIUtility.cs:179)