The subject question is really only a guess, as I’m asking it on behalf of someone else.
Based on what they’ve told me, they opened a .doc file from a usb flash drive and edited their document in LibreOffice Writer. They then saved the file in the default .odt file format. Opening the file the next time, they noticed that most of their 200+ footnotes were missing.
Which OS and LibO version is used?
Do your friends still have the original doc file? They better keep it save for the time being.
What exactly did they do when editing the file in Writer?
Could they upload the doc file? ( Be careful with the content of the file, this is a public site!)
Could it be that they changed footnote to end notes? Did they check if there are endnotes in the odt-file?
These are good questions, but this is more a comment than an answer, isn’t it?