Changes like renaming a file triggered by an app only appear to the USB-MTP interface after reboot of the Android device or after you registered the new fil
I ended up creating a dummy text file in each directory I wanted to make visible, and use scanFile on the file.
1) create directory, but don't "scan" directories
2) copy file to directory
3) run scanFile on the filePath
MediaScannerConnection.scanFile (_application, new String[] { filePath }, null, null);