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Is there anything I should expect to not work well when I replace the screen of an iPhone 12? Also should I expect any ‘ingenuine screen’ pop ups?

Things you can break include Face ID, True Tone, water resistance and anything else if you accidentally knock something off the board. You should expect “non-genuine parts” because Apple designed the phone to reject even genuine part if the repair is not registered on their server. Face ID and True Tone will work again if you register the repair with them via the self-service repair program. Water resistance may be restored if you use genuine screens and reapply the adhesive properly.