When saving a list of items if the class implements IsDeleted as a property and it is true, the item will be deleted when it is saved.
//Create a couple vendors
List<Vendor> vendors = new List<Vendor>();
Vendor vendor1 = new Vendor();
vendor1.Name = "Acme Rocket Motors Inc.";
vendor1.IsDirty = true;
vendors.Add(vendor1);
Vendor vendor2 = new Vendor();
vendor2.Name = "Acme Windshield Wipers Inc.";
vendor2.IsDirty = true;
vendors.Add(vendor2);
_ninjaDbPro.Save(vendors);
//Ensure they were saved
Vendor vendor1Copy = _ninjaDbPro.Load<Vendor>(vendor1.VendorID);
Vendor vendor2Copy = _ninjaDbPro.Load<Vendor>(vendor2.VendorID);
//Delete one
vendor2.IsDeleted = true;
_ninjaDbPro.Save(vendors);