Notes are missing
Notes were deleted
If a Note was deleted from the Fastmail interface, using undo Ctrl + Z or the undo link straight after deleting, will undelete it.
For Notes that were removed some time ago, raise a support ticket to have them restored from backup.
A known issue with Apple Notes
A few users of Apple Notes reported that all of their Notes went missing, and we had no record of their Notes in backups.
Unfortunately this seems to be a general issue with Apple Notes.
If the device hasn't properly shared the data to Fastmail or back to the Apple iPhone/Mac desktop, then the Notes go missing as if they were never saved at all.