I I have this situation too, and what I have noticed is when all the “off-line notes” are backed up, if you change one note in a folder or add a note, the off-line notebook never seems to update (at least by way of the progress bar).
However, as a test, I created a note When my iPhone was in airplane mode with Wi-Fi shut off, I could still view that note in this off-line mode.
So is there really a problem or is it just in the display of the progress bars uploading the off-line notes?