I've been facing same problem after last update, when my theme was somehow disabled by it and when I enabled it again I couldn't get my favicon back.
I found out it's because it is cached somewhere. I edited lib/private/URLGenerator.php and in function imagePath I commented path retrieval from cache (lines 147 to 149). After page refresh, there it was, my favicon.
Don't forget to undo all changes to this file afterwards.
Probably there is better way to achieve this.