I've done a massive work putting a lot of subtasks in a new folder. None of them are in this folder now. Instead of that they are in the wrong folder. Could be (must be) the Todo app on the iPhone. Awful.
Appigo Todo automatically puts sub-tasks into the same folder as the parent task - you can't change folder. So if you've moved sub-tasks to a different folder on Toodledo.com, the next sync with Todo will move them back. Nothing you can do about this - it's how Todo works.
I put all of my multi-step tasks into a "projects" folder to avoid this problem.