I've had similar issues with data imports before. Sometimes, it's about how the software interprets the format. Have you tried checking if the notes are formatted in a way that webtrees recognizes? When I deal with data discrepancies, I often use tools like [url]
notesonline.com/notepad
[/url] to review and adjust formats—it helps keep things organized and ensures compatibility across platforms. Hopefully, tweaking the format a bit might help those notes show up where they should.