Repro steps:
1. Install "Input System" package.
2. Import 2 of the available samples.
3. Create a new C# script file inside each folder from the samples folder up to the Assets folder.
4. Click "Import again" in the Package Manager UI.

Expected Result:
The sample is reimported correctly and no other files are affected.

Actual Result:
The Assets folder is deleted with any other files inside the project folder. There is a message in the console saying "Cannot delete directory <path to your project directory>". Unity is frozen while trying to fix all the missing files. Eventually, the editor starts to work again, but all deleted files were lost.