Having an issue - I'm generating webhelp with RH2017 (using customized version of Azure_Blue for output,) and as often occurs some of the artwork has changed as the project has progressed: the favicon being one of the changes. I deleted the old favicon and replaced it with the new one, but the old one keeps showing up in the HTML5 output. It's not a cache issue from what I can tell as other users who have never accessed the webhelp before are seeing the old icon as well when I post it up on a server.
Difficult one as you seem to have tried the usual things, different browser and so on.
The only thing I can think of is a longshot. I think 2017 internally renamed the favicon so with the same name, is it getting updated on the server? Check the image on the server really is the one you think it is.
Maybe try another layout and publish to a new location?
I notice reading again, you deleted the old icon. How? Did you just do that in File Explorer or did you browse to the new file from the layout?