Repro sptes:
-download this project
-the script upgrading dialogue will pop up
-notice when the project loads that the script will not be upgraded because of this error:

APIUpdater encountered some issues and was not able to finish.
System.IO.FileNotFoundException: Could not find file "D:\Unity\new A"
File name: 'D:\Unity\new A'

My project's name is: ''New A$''

Reproduced with: Unity 2018.3.0a8, 2018.3.0b5 and trunk
Not reproducible with 2018.2.1f1