[Adam B.]

It appears that notes and links are tied to the filename of documents. This means that if you rename a document, all notes/scribbles will no longer exist. You'll have to merge everything before changing the name.

This is a disappointment with the new contentlister. I like to have my documents neatly organized and labeled. There's no rename functionality built into the device. It also explains why they want you to manage it with the companion software instead of working directly with the file system.