I just upgraded to Android 4.1.1 Jelly Bean and I was wondering if syncing my Facebook contacts could mess up my Google Contacts (which are very well organized compared to facebook), or if both services do keep isolated from each other.
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No, they are run completely separate and exclusive from each other, not something that'll completely replace the data within your existing contacts... Although they can be merged so that it displays one contact instead of two (again, it still won't physically combine the data). That way, you can have their profile pic as a contact icon and even their birthday, phone number, email in one place if they have it on their profile. It'll try to merge automatically if the name + phone number or email from your Google contact matches what they have in Facebook, but it'll have to be manually merged if it doesn't.