I set the whole cache to disabled while making changes, and even then I still refresh it when things aren’t going as planned. I don’t think that was the problem, although Magento does some weird things when it comes to updating itself after code or layout changes.
I basically ended up installing a clean copy of the theme, overwriting my changed copy, and that did the trick. Now I’m reapplying the changes one by one. I’m still not sure what happened.