I have been doing all the hazardous stuffs with my Redmi Note 3, semi-bricked it and revived it again. What I experienced was, when I migrated from Dev ROM v5.12.24 to Stable ROM V188.8.131.52 by means of SP Flash Tool which wiped everything, it seem I had relinguished privileges of having Root Access and Bootloader Unlocked along the way. And mind you it is a non-permanent and fiasco thingy.
From, my personal observation, in order to acquire the Bootloader Unlocked, it is imperative to be done strictly with Development ROM.
The backdoor, is to have your redmi Note 3, Unlocked, then flashed TWRP and flash any other Stock or Custom ROM as required.
The other issue, yet a great feature, the security measure and keeping privacy tight, the Redmi Note 3 is the smartest among its silbings or big brothers, since with the implementation of Bootloader locked, is that WHENEVER YOU SUCCESSFULLY UNLOCKED YOUR BOOTLOADER USING REDMI NOTE 3 (UNIT #1) YOU ACTUALLY SIGN A MARRIAGE DEAL WITH IT UNTIL YOU FLASHED ANOTHER FLASHING TOOL.
YOU CAN ONLY ASSOCIATE YOUR ACCOUNT TO TWO UNITS OF REDMI NOTE 3 AT ONE TIME (I do not know of the future release of phones) THE THIRD ONE WILL BE REJECTED AS AND WHEN YOU RELEASED IT. To do so you need to fastboot locked to be able to transfer, give or sell it to another party, so it is a mimick of an APPLE ID situation, including to sign-out from “FIND DEVICE” equavilant of “Find My iPhone: on an iPhone.
SO NEVER SHARE YOUR VERIFIED BOOTLOADER UNLOCKED Mi ID WITH ANYONE.
My screenshot to give you a thinker, as shown below:-