Accidentally deleted handwritten notes on a pdf.

Hi everybody!

It's the first time I post, so be patient. I am a Ph. D. student and I have bought an iPad (10.9, 4th generation) to read and make notes on PDF documents. I use the Logitech Crayon. I open the PDFs in the app "Books". It works perfectly and, honestly, it is even better than what I expected when I bought the Ipad. Simply, it was THE solution I was looking for.

Though, I have a problem. Maybe it's just a misusage due to my inexperience with an iPad. Sometimes I accidentally delete the handwritten notes and highlighted passages with the Crayon during a session. This can be a major problem and it may cost hours of work. I noticed that sometimes it appears a pop-up message asking if I want to delete the added notes. Of course I answer no, but sometimes the notes seems to be accidentally eliminated anyway. I cannot understand what triggers such a message, how to avoid it, and, in case any notes have been accidentaly deleted, how to reverse the action.

Can someone please help me?

Thanks in advance for all who will answer.