Fortification does not protect units from loss of life during sieges, and in fact it seems to amplify it. Units take way more loss of life while under siege then they should, even while fortifications on the city remain, and they typically die within a turn or two, well before the walls come down.

Here is a thread I started on Steam, with several others sharing the issue:

http://steamcommunity.com/app/289130/discussions/0/208684375420567771/

I have tested, and confirmed, that this bug occurs on save files that existed before last weeks patch, and  also on games with Tempest disabled. Whatever y'all did, ya did it last patch.

I can't roll my game back to a previous version, anymore, because Steam disabled that feature a couple of years ago. Please fix this, I just dropped a lump of cash and bought ALL of your DLC, and the next day it was broken. I'm more than a little pissed, but I understand that these things happen. I hope that your team resolves this issue, soon.

https://www.games2gether.com/endless-legend/forum/115-bug-reports/thread/22161-siege-enemy-taking-damage-immediately-even-while-they-have-fortifications-left