Some of you may have seen this article already but if you haven't seen it yet chances are you will. This article refers to a guardian reporter who broke his iPhone while reporting in the Balkans, he decided to get the phone repaired while he was there as he needed the phone for work. When he returned to the UK his was notified on his phone that there was an iOS 9 update, he installed it as usual and that when he got the error 53. There are a few key points to note before panic sets in.
1) This error occurs when the touch ID sensor isn't reinstalled into the device either properly, partially or not at all (Some repair agent save time by installing fully assembled screens, this is true of a high street shoe repairer over here, this type of repair fits a different home button, and/or flex cable, both of which not only disable Touch ID but can also lead to the error 53).
2) The repair was carried out in the Balkans, the article does not explain the type repair that is carried out or the quality, he may have had the Touch ID sensor or the cable replaced entirely or most likely the flex changed as stated in point one, this is a "quick" repair if this is the case and not a thorough repair.
3) The Touch ID sensor in paired to each phone at the time of manufacture this has been the same since the fingerprint scanner was introduced in the 5S, damage the Scanner and replace it and the fingerprint scanner will no longer work. The difference in the iPhone 6 is Apple pay, the fingerprint scanner now allows for payments to be processed using your fingerprint as verification. Apple verify this at the time of upgrade and if the components fail the verification process then the error comes back. This is designed to protect your fingerprint and possible payment verification from being tampered with.
All the repairs that we carry out transfer as many original parts as we can reuse, so we buy new screens that are basically just the new screen and the touch digitiser like the image below (1):
We then transfer the front camera/proximity sensor & microphone flex, the original speaker, the EMI Shield (Large metal plate that give rigidity to the screen and carries the Touch ID flex) The Touch ID sensor and all the screws that held the original screen together, We have repaired over 30 iPhone 6 models in January and have had no issues.
This is the type of screen (2) that is fitted and that could lead to the error 53 issue. Everything is preassembled so all the parts that I listed that we swap are already on this screen. It is then just a simple can of swapping the entire screen assembly. This is where the problems come from, the Touch ID sensor and its flex may not be swapped, and even if it is swapped on the screen the chances are the flex for it isn't, either of these parts can the fail the verification process.
I hope this goes someway to explaining the issue, and also to calm some of the fears, we are a responsible repair agent and make our customers aware of the warranty implications, unfortunately stories relating to Apple always gain large attention but please don't panic. It is thought to convey a full and thorough explanation here but if anyone has any questions or needs any advice then please don't hesitate to contact me through the usual channels.