If you use ClearLinux’s mixin to add custom bundles to your installation, you will still be able to update your upstream bundles, however it will nolonger be as simple as doing a
sudo swupd update. Here are the step’s you need to go through, assuming you defined your mixin repository in
cd ~/mixin-repo createrepo_c . sudo mixin build sudo swupd update --migrate
… this is at least the process I have used, and which worked for me.