Reveiw the "joomla" templates that your are using.
The favicon.ico path is generally defined in the joomla template that you have selected.
So when you have different templates directory for each slave sites, you just have to change the favicon.ico that is present in your specfic "default" joomla template that you have selected for your slave site.
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So review the implementation of your selected templates and it will show you where it reads the favicon.icon (if this is not in the templates folders as most of the templates do it).
For example the favicon.ico of the standard ja_purity is located in directory
\templates\ja_purity\favicon.ico
So if you have put templates specific to each slave site, then this favicon become specific