I deferred an Aero and now my Time Notes are gone!

When you defer an Aero, your progress is saved. When you start working on the Aero again, you'll notice that any previous steps are checked off, but the Time Notes box is empty. That's because you are now creating a new time entry and it will have new time notes. 

Any previous time entries will be available under the Time tab at the bottom of the screen.
 

Any comments you made previously will still be in the Comments box, since they belong to the entire Aero, not just one-time entry. 

Note that if you don't actually defer the Aero – if you just pause it and close the tab, nothing is saved: What is the difference between pause and defer?