So, @con-f-use you were right: something must have changed in the meanwhile and the old method didn't work anymore.
I came up with this and switching backends seems to work: when using webkit you are greeted by a really helpful document that explain the reasons for not using it.

The problem with this is that qutebrowser on NixOS has been using the webengine backend for some time. This change suddenly changes to webkit by default, which causes the user to loose their sessions and breaks websites which were working just fine. It's not a big deal for us running NixOS unstable since we expect things to break sometimes, but when this change gets released it will be a problem for qutebrowser users.

Given the qutebrowser devs recommend using webengine, I think it's best to make webengine the default, while still allowing the option to use webkit.

Sorry, I messed up! I must have left "webkit" from when I was testing it.
Of course, wekbit should never be the default. I'll fix it ASAP.