We use Ultimate Branding to maintain various favicons for our subsites on two different WP instances (one IIS, one Apache/Linux). We just noticed that after the latest WP core update, the site favicons have now been replaced by the default WP icon.
I went into the Apache/Linux WP admin and tried various settings within Ultimate Branding's Images tab, but nothing is working to correct the issue. When I paste a path to a PNG image in the field for one of the subsites and click the row's Save button, it appears to save and the icon thumbnail is correct. But refreshing the page shows our own branded icon in the thumbnail column again (despite the correct path showing). If I click the Save Settings button at the bottom of the Images page, it reverts the path to our default branded icon's path as well.
And despite all this, even though our default icon appears within Ultimate Branding's Images settings, it is not used as the favicon for any of our sites on the front-end. They all have been reverted to WP's default.
I also tried toggling the setting for allowing overwriting the icon from Appearance > Customize, but it made no difference.