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I have a few devices I want to put back from custom roms to stock. On almost every stock rom source, however, there are dire warnings for some devices not to downgrade to stock versions from before your latest installed rooted rom version. For example, from Androidayos:

UPDATE: DO NOT DOWNGRADE back to the old stock firmware version. Once your Galaxy Note 2 already runs on 4.4.2 based rooted ROM you should only revert back to 4.4.2 stock firmware, same as it goes if you are on 4.3 you may install and stay on 4.3 and then upgrade to 4.4.2 KitKat but do not ever downgrade to 4.1.2 or 4.1.1 due to the current secured bootloader on every update.

I wish to really understand that warning. For example, if the bootloaders are secure, how is it so easy for people to flash custom roms for the first time, coming from those 'secure bootloader' stock firmware versions? What would actually happen and what problems would arise if one did downgrade just as is proscribed in the warning? If there's a "current secured bootloader on every update," why is it safe to flash the same version that one is currently running rooted, but downgrading is not? And so forth…

I'm doing this to several devices, but the best is example is a Samsung Note II currently running Cyanogenmod 12.1, which is 5.1.1 Lollipop. In that device's case, every stock firmware is an older Android version than Lollipop, since no brand pushed OTA updates beyond 4.4 KitKat. If I go back to stock 4.4.2 KitKat, I'm going 5.1 to 4.4—doing what they're warning against. How do warnings like that pertain to devices in this state, and what should I expect?

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Bootloader itself will get updated with some firmware updates. Take the Galaxy S6 as an example - the firmware G920FXXU4DPJN comes with bootloader level 4, while G920FXXU5EQF1 comes with bootloader level 5. Samsung has made it so you can only flash the same or a higher level of bootloader by official means, so as to prevent downgrading and exploiting vulnerabilities in older ones to achieve modifications such as rooting.

This bootloader level is not necessarily tied to the Android version of the firmware it comes with, although on older devices it tends to be the case - every major Android version bump comes with a new bootloader.

...why is it safe to flash the same version that one is currently running rooted?

Since bootloader is a rarely updated part, a series of updates will share the same bootloader level. Allowing the same level will let these updates through.

What would actually happen and what problems would arise if one did downgrade?

Attempting to downgrade will either stop halfway when flashing, or result in an unbootable phone (until you return to a firmware of the original bootloader level).

...how is it so easy for people to flash custom roms for the first time?

Bootloader has been unlocked by default on most Samsung phones (except AT&T, Verizon and a few other examples) up until Android 5.x, where the "OEM Debugging" switch has been added in the OS to ask for explicit user consent when they attempt to flash anything. Flashing under unlocked bootloaders are almost always easy and safe, but of course with the price of warranty void.

a Samsung Note II currently running Cyanogenmod 12.1

By definition you know that's not a stock firmware. In fact you probably shouldn't even call it firmware, since it only contains updated /boot and /system partitions - no userdata, no modem, no bootloader. Custom ROMs don't depend on bootloader level as strictly, and when they (rarely) do, they simply halt installation if the check fails, leaving you with an untouched system. More importantly, the bootloader itself is never modified or overwritten, so stock ROM compatibility stays the same - you still can only flash ones with the same or higher bootloader level.

TL;DR - bootloader level matters, Android version doesn't.

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