On your CTOS action can you check if you have the insert unique id checked or not?
If you check it you will see the device ID variable so this will then insert the same device id as used by your bare metal entry so when the full agent is installed will update the same record rather than creating a new one.
the CTOS step does include Insert Unique ID. Is there a preference to use MAC over Serial Number for the identifier?
The default variable is the correct one. If its not working when ticked I would try unticking this and see if that resolves the issue.
What version of LDMS/EPM are you running?