This kind action is also some short of resetting the phone firmware to it's original state. Of course firmware it's up to date with latest changes from Xiaomi. You may wonder there's no emmc_appsboot.mbn. The reason is there is no reason to flash nootloader every time. And by this way, your cuurent phone bootloader state stay still and unchanged. It mean if your phone is unlocked, it still remain unlocked.
This firmware commonly used for preflashing before Installing any Nougat based Custom ROM for example: LineageOS 14.1 ROM.
Download Updated CM14/14.1 firmware for Xiaomi Redmi Note 3
Choose firmware files matched with your devices below
Installing Redmi 3 Note Nougat
This instalation need TWRP recovery, and latest TWRP mod by TheStrix is recomended for the best result.
Put the firmware you've downloaded into your phone storage.
Reboot your Xiaomi Redmi Note 3 into TWRP recovery
Choose Install menu, locate your firmware and select the firmware and slide at the bottom to right.
Do a factory reset (data, cache and dalvik-cache)
And now you can continue proceed to installing Custom ROM Nougat based you desire.