Version of PDN in use is the Windows Store variant of paint.net 4.0.21 (Final PDN 126.96.36.19989.7045).
Operating system is Windows 10 Home (Version 1803).
When I save or edit a file in Paint.NET, it doesn't seem to take effect outside of PDN, in spite of the thumbnail reflecting changes in the "Save As..." and "Open" windows. That is to say, if I were to edit a file named "untitled.png", Explorer would still show the old verison of the file, and the old version of the file would be what was opened in other applications. Likewise, if I were to create a file called "untitled2.png", it wouldn't appear in Explorer. As with Explorer, the edits or existence of these "phantom" files will be completely ignored if I try to open them in other apps such as MS Paint or Photoshop.
In spite of this, all other applications in the same directory behave normally and all files from Explorer also appear in the folder. I have been able to delete "phantom" files made with PDN from the Save As... menu and have them appear in the Recycling Bin in Explorer, where they can be "restored" as normal.
Stranger still, when I try to delete a file while it's open in Paint.NET using Explorer it claims the file is being used by "System", which has me wondering if some kind of reading and writing permissions error might be involved.