Hi guys, so it happens to me too while testing various sMIUI versions. Using true dual boot it's easy to go in bootloop (sometimes i fail, sometimes system fails ^-^).
But i've never had to use MiFlash pc tool because i always solve problems.
First of all, i suggest you to buy Titanium Backup Pro, just in the extreme case you have to format data (sdcard will be not formatted). Also i have a copy of the Titanium Backup folder in my pc to be safe.
If it happens to you too to go in bootloop, you can just try to format cache partition (try with data later) and flash over a sMIUI or MIUI rom (i suggest you to flash the same rom you have already flashed before ON THAT SYSTEM). 90% of the times I go in bootloop i solve just flashing over another rom. This will make you lost ANYTHING.
If you are unlucky and this didn't work (try first this process to both system 1 and 2 first) you can always try to format also data. This worked 100% of the times FOR ME, but it will make you lose all apps you have installed and also systems settings. I know this is boring, but is where Titanium Backup comes up and saves you
You only have to configure your gmail account, open playstore and install Titanium Backup. You will notice that /sdcard was not formatted and all of your backups are already there
As you may know Titanium can also backup your settings, system apps, apps' data.
It never happend to me, but I understand that it could happend that both this metods didn't work. Search on google for a MiFlash guide that will make you completely restore your phone. You will lose every photos, videos, audios, and also Titanium Backup backups. This is where you will have to copy the Titanium folder from your pc to your Mi3/Mi4 /sdcard folder and just install back Titanium from the Playstore and restore back all your settings/apps+data
This is the risk you should already know it may happens while flashing roms, this is why developers always write that they do not take responsibilities
Hope I helped the ones who are stuck in bootloop
cya and happy new year
*Correct me if I made mistakes, thanks*