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Mark as Deleted is a field.
It basically indicates the Item has been deleted, but it still exists in the CMDB and the DB.
Nonetheless some tools (Atrium Explorer/Relationships menu) will ignore CIs/Relationships that are mark as deleted, so they are essentially already gone.
Delete can mean multiple things depending on the context, but normally to delete a CI or REL means to mark as delete it.
Purge is an action from the Reconciliation Engine that can permanently delete a CI from the CMDB, removing it from the DB.
Physical delete is when the CI/REL is actually deleted from the DB.
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Also, a PURGE job is usually used to "physically" remove CI's where the "Mark as Deleted" flag is set to yes and / or the Asset Lifecycle Status is set to "Delete".
I call the Mark as Delete flag and Asset Life Cycle Status of "Delete" as logical deletes. To physically remove the CI's you can either run a Purge Job using Recon engine or click the "Delete" button on the CI.