Would you please provide more information about your problem so that we can help you?
Where is the PDF document stored? Is it stored locally on your iPad/iPhone or cloud storage (e.g. Adobe Document Cloud, Dropbox, Google Drive)?
Would you check all locations to see if you have multiple copies of the PDF document?
Do you recall what happened before all the highlights and notes disappeared? Did you close the PDF document yourself by tapping the < (Back) button? Did you see an error message when you tried to close the PDF document?