I have a TP-Link Archer C7 AC1750 v5 router and I followed the instructions here to expand my filesystem space using a USB drive.
It works, but reading the guide I did not understand whether I will have issues when upgrading the system.
In general I upgrade the system by using System -> Backup / Flash Firmware -> Flash new firmware image from LuCI.
What I'd like to know is: will having this Extroot config break anything when upgrading the system via LuCI or not?
You can not upgrade extroot in any meaningful way.
You must redo whole setup after clean install with reset.
More comfortable option is to keep programs in flash but their data on usb
You can sysupgrade normally, that part works and is safe - however afterwards the extroot setup is gone and needs to be redone from scratch.
From a usability point of view, it is much easier to work without extroot, the archer-c7 has 16 MB flash which already is quite plenty - and these days there are routers with larger amounts of flash. Extroot is a kludge from the olden times, when neither money, nor good words could give you 'enough' flash - but it's best not to use it.