Service [Q] USB Not Working - Sony Will Fix, but...

The USB connection on my Z has broken and it no longer registers a connection for either charging or data transfer. Not a huge issue up until now as I just recharge using the dock and haven't needed a data transfer, but now I need to repair my installation of 4.3 as some things are buggered, so took the phone to Sony for them to have a look.

They agreed it was broken, which is a nice first step and said that they will fix it because it's under warranty but said that I would have to back-up everything I wanted as they couldn't guarantee that they wouldn't wipe the phone. I was wondering if anyone knew if this was likely to happen, or if it's just what they tell everyone who takes their phones in to get fixed as a standard advisory.

They couldn't explain why fixing a component on the top corner of the phone might affect the phones internal storage, but then I was talking to customer service and not the engineers. I've tried to back most things up, but without a USB connection it's mostly just transferring stuff to the SD or to the cloud, but I'm worried that I'm going to miss something important in the back-up process and was hoping if someone knew if I'd be safe if I just backed up what I could / what I could find, and not actually lose stuff during the repair process.

Thanks