Steps to reproduce:

• Open attached project
• "Assets/MyUiDocument.uxml" is invalid
• Edit the file with a text editor, and remove 

{code:java}
My Attribute="20" {code}
from line 2

• In Unity, open MyUiDocument.uxml with UIBuilder, change the value of "My Attribute" in "Custom Visual Element" and save

Result : "ghost" attributes are saved in the uxml from previous code and corrupt the file. The issuing one is : 
{code:java}
My Attribute{code}
Adding it to the list of obseleteNames doesn't remove it either.