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Don't panic yet. Maybe your notes haven't vanished. Exporting is supposed to save a copy. Your notes should still be on your ereader. If you click All Notes on the Home screen of your ereader, then you should still see them in the list.
There are 2 methods to delete notes. Do you remember doing either of these?
1) On the device itself through the various option settings.
2) When you open the book in the Sony software, there is a notepad icon in the lower left corner. Click that icon and it lists all of your notes. You have to select the notes, click delete and answer yes to the "Are you sure?" prompt.
It is likely that you have two copies of the book, and you are looking at a copy without notes. One copy is probably on your hard-drive and shows up in the Sony software under the Library icon. The other copy is on your ereader. The notes are associated with the copy on your ereader since that's where you made them. If you open the copy in the Library linked to your hard-drive, then you won't see any notes. You have to set-up the software to "sync" collections to transfer the notes automatically.
So how do you know which copy you are looking at? When a book is open in the Sony software, there is a little "i" button in the upper-left corner for "information". Click that button and it shows you the file path of where the book is located.
Hope that helps.
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