Finder comments disappear with external app modification

I am using and beta testing a forthcoming Markdown notes editor. I’ll leave the name of the application, since it’s not officially released yet, but it’s basically an app that managed notes in a standard filesystem folder. I have the same folder indexed in DEVONthink 3. If I modify any note in this application, the Finder notes metadata disappears entirely in DEVONthink, though it’s still present in Finder. Do you have any ideas what modifications may cause DEVONthink to remove the Finder comments in its database, while they’re still present in Finder?

Update: A developer of this product told that it should be fixed now with some change in metadata saving.

In which folder are these notes located? Do you use PathFinder?

They’re in some ~/Dropboxs/Documents/Notes folder. But the developer said that it probably has to do with the way their application writes metadata on save, and they’ve changed it in a forthcoming build. So if it’s true, then it doesn’t seem like a DEVONthink issue primarily.