Can I Populate Physically Deleted CIs from SM to UCMDB

No.

Physical deletions of CIs are allowed in SM, but SM cannot get such “deletion changes” and the population feature will not synchronize such changes to UCMDB.

Physical deletions of CIs can be considered as exceptions, which only occur after you create CIs by mistake. Normally, you delete a CI by setting its status to something like “Retired/Consumed”. If such CIs have been populated to UCMDB, it is your responsibility to remove them manually from UCMDB.