Hi Thilini,
My advice is writing an ABAP routine (e.g. Expert Routine) in a Transformation from the DSO to the same DSO (i.e. a loop over itself). Here you have to make the appropriate selection and then give 0RECORDMODE the value 'D' (i.e. delete). You only have to supply the key fields but non-key fields won't harm. This way the Change Log will register the deletions and can be used for delta mechanism towards subsequent InfoProviders. It also will delete the records from the Active Data table.
Best regards,
Sander