No issues with ConvertConfig.ini my end CustomAppsList.txt (to the best of my knowledge) has always been overwritten, you have to rename your custom list to CustomAppsList2.txt and it will then... be picked up by the converter and used as your preferred configuration.
Is there some way to convert UUP Dump stand-alone updates into one MSU package? NTLite doesn't recognize stand-alone files like DesktopDeployment.cab, but has no problems recognizing such within LCU MSU packages. Does W10 recognize stand-alone CAB files from UUP Dump? EDIT: W10UI doesn't recognize them either - error 0x800f081f regarding source files. It doesn't do that with official LCU packages.