As stated, it happens in both Cycles rendering and Blender engine rendering. It is however CPU rendering, I am unable to test GPU rendering. For your other pointers, I did not try those (I'm fairly new to Blender). What fixed my issue was changing my rendering output from PNG to JPG by accident. This caused the rendering to start over from the beginning (no image sequences in that format). When I changed it back to PNG now with Overwrite still unchecked in the Output menu, everything worked fine again. I immediately saved the .blend file in this condition which is why I refrained from publishing it.