Nikon released Capture NX-D (Mac) Version 1.3.1 with a fix for the files deleting issue I reported on few weeks ago:
Renaming folders created in root directory (under startup disk) has been made unable in order to prevent images stored in the folders from being deleted.
The latest ViewNX-i & Capture NX-D (Mac) Version 1.15.120 instal can be found here (this combined package installs the latest ViewNX-i and Capture NX-D versions together).
