I'm honestly not sure. This is getting into some grey area that I haven't been able to test into that much, due to how things are set-up where I work. This kind of sounds like a session memory type issue, like now that the hard copy file has been switched out, the old settings are still being held in memory, but they need to be flushed and the new settings need to be read into memory, but I'm not sure. I know of a couple 'memory' cleaning commands, but I don't know if they would help any in a situation like this.
For instance, you can supposedly 'free' or 'clear' up iLogic's memory with this command:
ThisApplication.CommandManager.ControlDefinitions.Item("iLogic.FreeILogicMemory").Execute
...and here is another sort of related command:
ThisApplication.CommandManager.ClearPrivateEvents
...which I think does the same thing as this one:
ThisApplication.CommandManager.ControlDefinitions.Item("iLogic.ClearCodeClipboard").Execute
...but that last pair just don't sound that useful. There may be something similar for the main Inventor application, but I can't remember right now. I know about the codes for importing the main application options, and the settings for 'use Inventor settings', as apposed to 'use Autocad settings', but I don't know if messing with them would cause any different 'memory dump & reload' type reaction.
Wesley Crihfield

(Not an Autodesk Employee)