This is actually an issue with Agent.exe, since use of Sysinternals Procmon.exe clearly indicates it’s the guilty program, but please ELI5 why Agent.exe objects to …\World of Warcraft\_retail_\WTF and …\World of Warcraft\_retail_\Interface\AddOns being NTFS Junctions.
I have it set this way as part of my backup strategy: those two folders are mapped elsewhere on my drive, under \Users\<myname>\AppData\Local if it makes a difference, so that they are automatically included in my nightly backup.
Every time Agent.exe tries to update, it comes along and deletes these two Junctions, which needless to say proves very inconvenient. At the current time I have a working solution to prevent this, but it really should not be necessary.
Respectfully Blizzard, it’s none of your damn business where I put these: the view that World of Warcraft has looks correct, the game functions fine. Why do you care?