Tremor, first let me say I don't think williamcopper's reference to bounce to clips applying forced MIDI channels to event data has anything to do with this.
It seems you are saying that MIDI port, channel and patch assignments in tracks are reverting to None when re-opening a project saved as a bundle file; if that right? Or is it only the port assignments that are getting dropped?
I don't use bundle files (I prefer .ZIP), so I'd have to check that, but i don't recall any previous reports of an issue with this. This information is saved in the project (CWP) file that is part of a bundle file, and I've had no issue with projects recalling MIDI Express XT output assignments in X3.
Please indicate whether this is also happening with CWP project files, and give an example of exactly what the track headers show before and after closing and re-opening the project or bundle.