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I have a Honor 5X which I am planning to root so that I can flash Cyanogen MOD 13 as EMUI isn't up to my expectations(NO OTG and Adoptable Storage). Is it possible to flash the ROM then unroot my device to retain the warranty and have access to banking apps? Thanks!

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When you unlock the bootloader on a Qualcomm device it blows a fuse (an irreversible procedure). It does not matter if you even root your device afterwards - the damage is already done and the warranty is already void.

Then it all depends on on how strictly and diligently the customer service people follow company policy. For example once the device is unlocked it could be flashed with a ROM specifically modified to report its status as "never tampered with" - that could fool some less experienced folks.

As for the banking apps - it depends on the implementation. If done right the device would lose all its pre-provisioned crypto keys.

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