This possibly being a bug aside, I for one would never, never, ever, rely on checkpoints as any kind of substitute for Git, any more than I would rely on my clipboard’s undo / redo in a text document, nor Adobe’s “History” pane in a Photoshop file over the entire lifecycle of any project. (I guess some people might? I’d honestly never give that a second thought).
As to the timeline, there is a way actually, you need to create a new blank file for what was previously removed, in the previous location. See my other comment here: Lost 2000 lines of code because Cursor killed my file and rolling back via checkpoints does not work - #8 by jchase