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The root of bug #1508 is that it is very hard to get the corresponding MSBuildItem item from a ProjectItem. All ProjectItems which are procossed by the
MSBuildProjetHandler.SaveItem (MonoDevelop.Core.IProgressMonitor monitor, MSBuildSerializer ser, MSBuildProject msproject, object ob, Dictionary<string,ItemInfo> oldItems)
method are currently being duplicated in the Project due to Project.AddNewItem being called without any kind of checking to see if the item is already in the project. The 'SaveProjectFile' function works around this by having a customised 'AddOrGetBuildItem' method which it calls.
This sort of functionality should be baked in to completely eliminate this bug. This would also remove the need for the (broken) remove duplicates check in MSBuildProjectHandler.SaveItem (currently about line 958 which starts with "// Remove old items". This is the check which failed to remove the duplicate WebReferences as it only checked duplicates based on MSBuildItem.Name and Include which was not enough.
All this is fixed in XS 6.0