How to reproduce:
1. Open attached project "Updated.zip" project (which was previously opened with 2018.3)
2. Delete the packages that cause Compile errors from the Project Library
3. Wait for the recompilation process to end
-- Multiple 'error CS1704' messages appear that prevent from entering Play mode.

Reproducible with - 2019.1.0b8, 2019.1.0b9
Not reproducible with - 2019.3.11f1, 2019.1.0b7, 2019.2.0a10

Errors thrown:
error CS1704: An assembly with the same name `UnityEngine.UI' has already been imported. Consider removing one of the references or sign the assembly
D:/Unity_Versions/2019.1/2019.1.0b9_f1481f10a935/Editor/Data/UnityExtensions/Unity/GUISystem/UnityEngine.UI.dll (Location of the symbol related to previous error)
D:/Unity_Versions/2019.1/2019.1.0b9_f1481f10a935/Editor/Data/UnityExtensions/Unity/GUISystem/Standalone/UnityEngine.UI.dll (Location of the symbol related to previous error)

Notes:
- The issue is no longer present after repeating the same steps on the same version (reopening the project and deleting the packages).
- On 2019.1.0b7 and 2019.2.0a10 the package Compile errors (as mentioned in step 2) are not present.
- The issue occurs after deleting "Library/PackageCache/com.unity.multiplayer-hlapi@1.0.1" and "Library/PackageCache/com.unity.textmeshpro@2.0.0" (step 2)
- On 2019.1.0b8 only "Library/PackageCache/com.unity.multiplayer-hlapi@1.0.1" causes compile error (step 2)