if i get your question correctly, you converted a physical machine to VM, and added VM to the domain, without changing the hostname or sid. and then you find the physical machine is not in domain.. ?
SID doesnt change by itself, it can be due to someother reason, that your physical machine get lost access to the DC. After all you are not doing anything on your physical box, during the entire conversion process. check the event viewer on the physical box and see the errors there.