This may be CND specific.  Somewhere along the road, some of my projects ended up with duplicate logical folders, such as the source root or "Important Files".

To fix this I ended up editing nbproject/configurations.xml to remove the duplicates. If I followed this procedure:
 - close the project
 - edit nbproject/configurations.xml; save
 - reopen the project in NB
Then NB recognized the change.  However, if I did not close the project, then NB would ask to reload, but clicking "yes" did not change the list of folders. If then I close and reopen the project, the list of folders becomes correct.

Do this:
 - edit nbproject/configurations.xml, duplicate Important Folders.  Mine looks like this:
    <logicalFolder name="ExternalFiles"
                   displayName="Important Files"
                   projectFiles="false"
                   kind="IMPORTANT_FILES_FOLDER">
      <itemPath>gxf.nb-Makefile.mk</itemPath>
      <itemPath>gxf.nb-Makefile.mk</itemPath>
    </logicalFolder>
 - open the project, note the presence of two Important Files folders.
 - edit nbproject/configurations.xml, remove the duplicate folder.
 - NB prompts to reload the project, but the number of folders does not change.
 - close and reopen the project and the number of folders is now correct.

Personally, I have seen issues like this for years with NB: the lack of synchronization with the state of NB projects in memory vs on disk. This one was easier than most to describe.