The update mechanism is designed to update the favicon. There’s no way for it to know whether you want to keep the old favicon or not so it always updates it to the latest one.
I think that in most cases people would want the favicon to be updated at the same time as updating other parts of the login. If you prefer to manually manage every favicon in your database and therefore do not want the latest one from the website installed, you should be able to disable saving favicons entirely but a quick look through my local source code suggests that no longer works so unfortunately that probably won’t help in the short term.
You should find that KeePass retains the old favicons though so if you prefer the old logo for a website you can always edit the entry from within KeePass and switch back to the one you like better.