How to reproduce:
1. Open the attached "1101384_repro.zip" project
2. In Project window, right-click on "Packages/2D Animation"
3. Select "Delete"

Expected result: Deleting "2D Animation" package via Project window is not permitted, or it is not visible right after being deleted.
Actual result: Although the "2D Animation" package folder is deleted, it is still visible in the Project window. Sometimes the Editor also becomes unresponsive.

Reproducible with - 2018.2.0b1, 2018.2.17f1, 2018.3.0a1, 2018.3.0b11, 2019.1.0a1, 2019.1.0a9

Notes:
- Could not be tested on versions prior to 2018.2, since the above mentioned "Packages" folder was introduced in 2018.2.
- The above-mentioned package "2D Animation" was installed not via Package Manager, but added manually to the Packages folder in the project directory. The issue is not specific to only this package.

Fixed in 2019.2.0a2
Backported to 2018.3.5f1, 2019.1.0b2