The registry folder or files under the $CPDIR/registry are attributed with the 'i' flag (Immutable - Prevents any change to file's contents or metadata: file/directory cannot be written to, deleted, renamed, or hard-linked).
This is rarely caused by a failed backup/MDS_backup but is mostly due to human error.
This will not allow the new cert to write the SIC name to the registry file properly on the machine you fail to initiate SIC with. (not on the Management server.)
When the scenario is on Multi-Domain Server/Multi-Log Management, you can see the issue on the customers context:
# mdsenv <CLM/CMA_IP>
# cd /opt/CPmds-R80.xx/customers/<CMA_NAME>/CPshrd-R80.xx/registry
To confirm the issue run the following command in the path according to your version:
# lsattr /opt/CPshrd-R80.xx/registry/HKLM_registry.data
The output is, for example in a correct situation:
Verify the same on the directory itself:
# lsattr /opt/CPshrd-R80.xx/registry