Also update Clover to the latest using the Clover installer. Be sure to fix EFI/Clover/kexts, so that only EFI/Clover/kexts/Other is existing. All version specific directories under EFI/Clover/kexts should be removed.
Also update config.plist at EFI/Clover/config.plist to the latest content from the repo. Be sure to retain your own SMBIOS data at config.plist/SMBIOS.
Now you can update via the App Store. Just boot the installer/updater upon restart.
After updating, run ./install_downloads.sh again: