You can use the wp_head action to print code in the <head> block of each document. If your theme does not use the wp_head() function, then dropping do_action( 'wp_head' ) into your <head> block is required.
Simplest way would be to wrap the favicon’s URL in a filter, and then change that depending on the current post being viewed. Note you’ll likely need to take measures to prevent caching of the favicon, which in my experience can be a challenge.
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