All,
Verified Solved with help from nealius. If you take your custom loadouts that you have saved in \Saved Games\DCS.openbeta\MissionEditor\UnitPayloads, and put that acft specific lua in whatever core mod root folder for the specific aircraft, Ex. \PROGRAM FILES\DCS World OpenBeta\CoreMods\aircraft\FA-18C\UnitPayloads, it will get rid of the stock configs.