The only way I can see Vanilla at fault is if the particular icons that disappeared are packaged through vanilla. While there are icons that ZOS can add and edit for the webpage theme, the icons such as the edit button are entirely from a single file location that only vanilla has access to and users can't change on their sites. So if someone from Vanilla mucks with or deletes anything with that file, it makes the icons fail to load and we're left with invisible icons. Which is really weird that they did that? I've ran my own websites and most of them give you the tools and it's pretty much on you to fix.
They do have a support section that apparently will resolve all issues in 10 minutes. So I'm not entirely certain why this is still an issue?
https://success.vanillaforums.com/discussion/4232/a-new-support-communication-channel