Deleting a Preboot image (winpe) are not deleted from the system and re-appear when you open the preboot menu again.
The Database had those entries and we needed to remove them via SQL query.
We used the following SQL queries to remove the WinPE from the Configuration Page :
Once we retrieved the GUID inserted it into ItemToDelete table and then ran the NS Daily task.
In this manner we were able to delete the items which were no more available into Menu list as well as Folder Structure.