[Zubersoft]

If you remove pages with the page order, those annotations are deleted because you've removed the pages they were associated with. You instead should long press the song on the library screen, tap "Copy Song", then modify the copy and add that to the setlist instead. This will preserve the original song. In the future, I will add support for song versioning so that you could just create a second version of the song to add to the setlist (this is planned for next year). You can also embed the annotations into the PDF itself, so then if you remove pages in the page order, the annotations are preserved as they are in the file itself.

If you want to recover your annotations, you have to go to Settings->Backup and Restore->Restore Automatic Database Backup and revert your library back to an earlier point. A backup is created every three days, so hopefully there is a recent one you can restore so that you won't lose much. 

Mike