I'm running MultiUpdater through HBL - running the MultiUpdater option in MultiUpdater installs the cia version and does not update the .3dsx version. Maybe have MultiUpdater check if it's installed as a cia. If it's installed, install the new cia, if it isn't, update the .3dsx. Other easy option is to split the MultiUpdater option in the menu into the cia and .3dsx version.
I'm running MultiUpdater through HBL - running the MultiUpdater option in MultiUpdater installs the cia version and does not update the .3dsx version. Maybe have MultiUpdater check if it's installed as a cia. If it's installed, install the new cia, if it isn't, update the .3dsx. Other easy option is to split the MultiUpdater option in the menu into the cia and .3dsx version.