There have been a ton of posts here about your issue and similar linked project location issues so a forum search will help with that. This blog post by Steve Stafford is a good starting point for you.

Edit: and this post this morning in Revit All Flavors/Blog Feeds, again by Steve Stafford may also be helpful

Who is "we", if I may ask? You can answer generically of course.

Were you involved in the earlier decision making required for model alignment? Did you create any of the models?

I ask because if you weren't then they may not line up automatically when you link them together again, fresh. It is possible that they linked each others models and moved them into position manually and left them as is.

If the model to model relationship existed prior to your involvement then you should find that the architecture file just can't find the MEP file and vice versa. Fixing the path to the MEP (and the reverse in the MEP model) ought to resolve that. In other words the alignment exists, you just need to help Revit find the file.

Diagnosing this stuff when you're looking in from the outside is a bit like archeology. Lot's of guess work unless you can actually talk to the people that built it in the first place.

Quick and dirty - link it in. Align levels and grids - move on.
If you need it more than just Revit, then you'll have to dig a little and sort out the shared coordinates.