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 ~/mixin-repo:

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.