That is very strange. I suspect that it successfully removed all node-entry relations, but fails to commit other changes, so the entry still exists, but without any node-entry relations it would appear as direct child of catalog.

Is the exception the same if you delete the entry when it's still in the category (aka node)? I would guess it's the same 

Yeah - same exception. 

I don't know if it matters, but we're using a multi-warehouse implementation. Variants never have stock on more than one warehouse though. 

Can you download this file https://www.dropbox.com/s/t6dsb86gnhvx0r4/Mediachase.Commerce.pdb?dl=0 , put it in bin, try to delete an entry and post the full exception stacktrace here? 

Sure, here's the full stacktrace:

Value cannot be null. Parameter name: code
at Mediachase.Data.Provider.TransactionScope.ExecuteActions(IEnumerable`1 actions) at Mediachase.Data.Provider.TransactionScope.ThreadStaticTransactionScope.Commit() at Mediachase.Data.Provider.TransactionScope.Complete() at Mediachase.Commerce.InventoryService.Storage.InventoryDatabase.DeleteInventory(InventoryKeySet partialKeys) in D:\BuildAgent\work\3a59b0e2f981838\ECF\Mediachase.Commerce\InventoryService\Storage\InventoryDatabase.cs:line 210 at Mediachase.Commerce.InventoryService.Storage.InventoryCache.DeleteInventory(InventoryKeySet partialKeySet) in D:\BuildAgent\work\3a59b0e2f981838\ECF\Mediachase.Commerce\InventoryService\Storage\InventoryCache.cs:line 122 at Mediachase.Commerce.InventoryService.InventoryServiceProvider.DeleteByEntry(IEnumerable`1 catalogEntryCodes) in D:\BuildAgent\work\3a59b0e2f981838\ECF\Mediachase.Commerce\InventoryService\InventoryServiceProvider.cs:line 185 at Mediachase.Commerce.Catalog.Managers.CatalogEntryManager.DeleteCatalogEntry(IInventoryService inventoryService, Int32 entryId, Boolean recursive) in D:\BuildAgent\work\3a59b0e2f981838\ECF\Mediachase.Commerce\Catalog\Managers\CatalogEntryManager.cs:line 427 at Mediachase.Commerce.Catalog.Impl.CatalogContextImpl.DeleteCatalogEntry(Int32 entryId, Boolean recursive) in D:\BuildAgent\work\3a59b0e2f981838\ECF\Mediachase.Commerce\Catalog\Impl\CatalogContextImpl.cs:line 889 at EPiServer.Commerce.Catalog.Provider.Persistence.EntryContentBaseCommitter.Delete(ContentReference contentLink) at EPiServer.Commerce.Catalog.Provider.CatalogContentCommitterHandler.Delete(ContentReference contentLink) at EPiServer.Commerce.Catalog.Provider.CatalogContentProvider.Delete(ContentReference contentLink, Boolean forceDelete) at EPiServer.Core.Internal.DefaultContentRepository.Delete(ContentReference contentLink, Boolean forceDelete, AccessLevel access) at EPiServer.Commerce.Shell.Controllers.DeleteController.Delete(IEnumerable`1 contentReferences) at lambda_method(Closure , ControllerBase , Object[] ) at System.Web.Mvc.ActionMethodDispatcher.Execute(ControllerBase controller, Object[] parameters) at System.Web.Mvc.ReflectedActionDescriptor.Execute(ControllerContext controllerContext, IDictionary`2 parameters) at System.Web.Mvc.ControllerActionInvoker.InvokeActionMethod(ControllerContext controllerContext, ActionDescriptor actionDescriptor, IDictionary`2 parameters) at System.Web.Mvc.ControllerActionInvoker.<>c__DisplayClass15.<InvokeActionMethodWithFilters>b__12() at System.Web.Mvc.ControllerActionInvoker.InvokeActionMethodFilter(IActionFilter filter, ActionExecutingContext preContext, Func`1 continuation) at System.Web.Mvc.ControllerActionInvoker.<>c__DisplayClass15.<>c__DisplayClass17.<InvokeActionMethodWithFilters>b__14() at System.Web.Mvc.ControllerActionInvoker.InvokeActionMethodFilter(IActionFilter filter, ActionExecutingContext preContext, Func`1 continuation) at System.Web.Mvc.ControllerActionInvoker.<>c__DisplayClass15.<>c__DisplayClass17.<InvokeActionMethodWithFilters>b__14() at System.Web.Mvc.ControllerActionInvoker.InvokeActionMethodFilter(IActionFilter filter, ActionExecutingContext preContext, Func`1 continuation) at System.Web.Mvc.ControllerActionInvoker.<>c__DisplayClass15.<>c__DisplayClass17.<InvokeActionMethodWithFilters>b__14() at System.Web.Mvc.ControllerActionInvoker.InvokeActionMethodWithFilters(ControllerContext controllerContext, IList`1 filters, ActionDescriptor actionDescriptor, IDictionary`2 parameters) at System.Web.Mvc.ControllerActionInvoker.InvokeAction(ControllerContext controllerContext, String actionName) at System.Web.Mvc.Controller.ExecuteCore() at System.Web.Mvc.ControllerBase.Execute(RequestContext requestContext) at System.Web.Mvc.ControllerBase.System.Web.Mvc.IController.Execute(RequestContext requestContext) at EPiServer.Shell.Web.Mvc.ModuleMvcHandler.ProcessController(IController controller) at EPiServer.Shell.Web.Mvc.ModuleMvcHandler.BeginProcessRequest(HttpContextBase httpContext, AsyncCallback callback, Object state) at System.Web.Mvc.MvcHandler.BeginProcessRequest(HttpContext httpContext, AsyncCallback callback, Object state) at System.Web.Mvc.MvcHandler.System.Web.IHttpAsyncHandler.BeginProcessRequest(HttpContext context, AsyncCallback cb, Object extraData) at System.Web.HttpApplication.CallHandlerExecutionStep.System.Web.HttpApplication.IExecutionStep.Execute() at System.Web.HttpApplication.ExecuteStepImpl(IExecutionStep step) at System.Web.HttpApplication.ExecuteStep(IExecutionStep step, Boolean& completedSynchronously)

I can't see anything obvious, do you have anything listen to CatalogKeyEventBroadcaster.InventoryUpdated?

We did indeed have a listener for InventoryUpdated, I never thought about this triggering when deleting a product! Adding a check to the event listner solved this. 

Quan to the rescue again :)