The bug can be reproduced without old projects at all. In any project in 2018.3:

1. Create a new Canvas
2. Create a new Canvas as a child of the previous Canvas
3. Notice the child Canvas scale is 1,1,1
4. Drag the child Canvas to the Project Browser to make it a Prefab
5. Notice the child Canvas Prefab instance scale is now 0,0,0
6. Open the child Canvas Prefab Asset in a text editor
7. Notice the localScale of the RectTransform is 1,1,1

See comment in case for how to check that the library representation scale is 0,0,0 even though it's is 1,1,1 on disk.

Original repro steps:
When upgrading a project from Unity 2018.2 to 2018.3, some of the UI prefab scale was changed to 0.

1. Download attached project
2. open it with Unity 2018.2.0f2
3. Open the MainMenu scene from SceneAssets/Scenes
4. Notice the Canvas Hierarchy -> Main Menu panel scale is 1 and UI is visible
5. Open it with Unity 2018.3.0a6 or a7
6. Open the MainMenu scene from SceneAssets/Scenes
7. Notice the Canvas Hierarchy -> Main Menu panel scale is 0 and all UI is invisible