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As mine was swapped out for a new phone I needed to reinstall the lot from fresh - upgraded to the 50GB iCloud for 79p a month before going in and did a big back-up.
I think if they had managed to replace the battery my data would have been fine, as the guy picking his battery replaced phone up next to me still had the wallpaper and everything as handed in.
Worth backing up, basically.
Just over three weeks to get your battery replaced for £25...back up to £45 in January.
Got my iPhone SE (bought mid-2016) simply swapped for a new one yesterday as they said they had issues when trying to open it up, which was a result - whole process was around two hours from dropping off to being available to pick up.