Not the first instance of this happening on this forum, which is scary. I remember on a podcast a year or so ago Marco Arment and the ATP gang said they use Apple Notes, but “don’t store anything in there you don’t want to lose”.
I’ve been tempted (and have) made the switch to AN a few times, but cases like these make me super uneasy.
Make it a tool that stores your stuff as well-known and common file types in the operating system. That’s my recommendation. I understand that Apple Notes is an app that you can export from, but if the data goes missing, you have nothing to export.
Notes is pretty well supported by Shortcuts. I have not tried it but it would probably be fairly straightforward to write a Shortcut that on a schedule exports all notes to Devonthink or Dropbox or whatever other location of choice you wish.
One could consider such a shortcut to be part of a reasonable backup plan. However, for me, if Apple Notes were unreliable enough to require periodic and continuing export to a well-known and common file format, I would export once and be done with Apple Notes.
Until the root cause of the reported problem has been identified, and data confirmed to be unrecoverable, I would wait and see.