It's hard to say. It looks like they added it to the Retroarch menu at least, but it's not useful for the importer unless it's accessible from the command-line.
Yeah, this should be rare, but Windows doesn't handle those situations very well all the time. The update check only happens on startup, so it should only be a thing if you rush into something right away while it's still scanning for updates. I don't really have a solution for it other than to just not use a popup for it at all and replace the whole UI.
If it's only affecting the one platform, then my guess is maybe that the media folder path changed somehow for that platform? If you edit the platform, are the folder paths correct?