Skyline is not recognizing data acquired in negative mode (negative chemical ionization GC-MS/MS) from MassHunter. It is going to import only by setting positive charge to all transitions (all were acquired in negative mode).

At 8:31 PM:
Failed importing results file '\\fleuryfs\IPD\CROM\CG\20161114-02.D'.
This document contains only negative ion mode transitions, and the imported file contains only positive ion mode data so nothing can be loaded.

Fixed in 3_6 branch, merged to trunk. We were not properly noting the transition polarity for Agilent chromatogram data.