Will deleting the photos from my phone mean that the ones in my Favourites Album will be deleted too?


Short answer: Yes. At least for iOS9.

A bit longer answer: The Favorites Album in the Photos App in iOS9 generates a link to all photos that is marked with a "heart". If you delete the photo then the link in the Favorites album also disappears.


Yes, if you delete a photo from your Camera Roll that photo will also be deleted from all other albums, including the Favourites album.
Photos in a album is just a link to the photo in the Camera Roll.

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