Hello GhostintheFlesh,
Thank you for using Apple Support Communities! I understand from the information you provided that you deleted notes, and they were deleted from your device as well; I'd like to help.
Just to verify, you're using the steps found in this article:
If you're missing notes on your iPhone, iPad, or iPod touch - Apple Support
If you didn't use theses exact steps, tell us exactly how and where you deleted your notes. Did you do this a iCloud.com?
Keep in mind that you can also sync your notes to another service, like a Gmail or a Microsoft Exchange account. If you're syncing your notes to iCloud or another similar service, and you delete them, they will be removed from your device and the service. If you syncing your notes someplace else, you would have to look there to see if they have a recently deleted folder.
Hope this helps.
Best Regards.