Installer no longer creates EFI/org.clearlinux in /boot/efi

Clear Linux has a mechanism to only mount /boot when it is needed to avoid corruption. By default, nothing should be in /boot. In rare cases, I’ve seen where files end up on the root partition underneath. When this happens even though they appear under /boot they aren’t on the correct partition and this can cause problems.

Check the contents of /boot.
Make sure mount | grep boot shows the sda1 partition is actually mounted to /boot
If not, run systemctl start boot.mount
Check /boot again

Here is a more comprehensive post on the subject: