The problem may be that the notes are still there, but aren't visible when you search for them.
For example, here are some notes tagged with "Finland." Three of them in the attached screenshot mention a company, KWH Pipe, in the title. Yet when one searches "KWH Pipe's Working Hours Experiment" (the title of the second note in the list), the search comes up empty, and a search for "KWH Pipe" finds only one note.
This is not exactly the same as notes being completely gone from the database, but functionally, if they can't be found except through lucky manual labor, they're as good as gone.