You're totally right. I must have been very sleepy yesterday when I disabled story.checkpoint and believed that the savegame stopped working. I did it again and yeah, it's totally unrelated.
So I looked again and found the actual code for my autosave. Guess I really need to comment my code better.
My JS is limited but Snowman is my only option (my Harlowe design killed any mobile) and I'm kinda getting through it with the awesome help from this forum.
So sorry, and thanks!
PS: for the record, this is my autosave code:
localStorage.setItem( 'autosave', JSON.stringify( story.state ));