Are the notes still in the original UnfiledNotes section? Have you tried
opening a backup?

The recommended way to move UnfiledNotes is to go to the section that
you want to move, go to File->SaveAs, then pick the new location and
save the section as "Unfiled Notes". After that, go to
Tools->Options->Save, select unfiled notes in the paths box, click
Modify, and point it at the new section that you just saved. You can use
this method to point any number of instances of OneNote at the same
unfiled notes section, and it'll sync and merge just like any other
notebook.

Ilya