Renaming a file does not immediately trigger an update to the file name in data.json. This means that renaming a file, changing it's order, then reloading Obsidian (triggering a cloud save, closing and opening Obsidian, etc.) will result in the file moving back to it's original order.

Example:
I frequently will create a new file, move it's order (my hand is already on the mouse after creating the file, so might as well drag the file into the right position), rename my file, write down a sentence or two, then sync or close Obsidian. Upon reload or upon reopening Obsidian, the file is in the wrong position, but the name is kept. I must move the file once again and then there is no issue.