This is an accepted solution.
Nick here from Shopify!
That does seem very strange for sure! You mentioned you didn't update the theme recently in any way, but did you alter or edit the code at all or did you add any apps to your store? Could you also let me know the name of the theme you're using too, please.
Currently we can't look further into account/ theme specific issues via the community for privacy and security reasons. Because of this, if you're using a free Shopify developed theme your best bet would be to reach out to our support team here and contact our theme support team to see what might be going on.
However if you're using a paid third party developed theme, it would be better to contact the developer directly as they wrote the code for the theme and would know it best! They can take a look into this and see what might be happening with the favicon.
Hope this helps and let me know if you have any other questions!