Hi, David125, and everyone else,
This is a great discussion with a lot of good ideas about workflow, so thanks to all you helpful Revit users! Apart from the workflow issues, I'm still wondering if there is an issue with the model itself. David125, you didn't mention if you tried changing the arch view to fine? As scott.dakin suggested, it appears that the mech view is in fine detail, and the arch view is in coarse. You can see the one-line representations of the tees and elbows in the arch view, though not for the straight runs. Did this make a difference? It's also possible that the view from which you took the screenshot in the arch model is corrupted. You might try creating a new view to see if there's a difference. (Don't duplicate the existing one as it will also duplicate any errors that may exist in the view.)
Also, is the MEP link displayed by host view or by linked view, or does it use custom settings?
Just to cover another technical possibility, sometimes strange graphic things happen when your temp folder is full, and maybe that's a factor here. To empty it, please close all Revit sessions first. Then, in the Windows Start search box, type %temp% and delete everything inside that folder (there may be a few things that can't be deleted - that's okay). Then empty your trash. Does this make a difference? Even if not, it's a good thing to do once a week or so.
Let me know if any of this is helpful.
Cheers,
Judy Staicer