Thanks for the reply @bep!
Your guess was correct: it broke for me between version 0.31.1 and 0.32.1. I now also found the problem: having an index.md file in the content folder somehow broke the rendering. Renaming it to _index.md and replicating the single.html layout as index.html layout according to Render index.md as single fixed it.
I still think the behavior is a bit strange. It somehow worked (I got my index page served) and it also worked when moving files around while having live reload enabled. But it didn’t when doing a normal render run.
I don’t know if you could catch the edge case and print an error/a warning to the console in this case? Would have saved me a few hours and maybe would help others too.
Thanks again
Simon