Deleting a project from the Epic Games Launcher will also delete any files that are located in external folders that the project includes via symbolic link. In this case the only thing that should be deleted with the project is the symbolic link itself, and any files within the external folder should remain.
RESULT:
All of the files within the new folder have been deleted.
EXPECTED:
The symbolic link within the project's Content folder is deleted with the project, but all of the files within the linked folder remain in that folder.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-53966 in the post.