That is an odd duck. If they are not intended to modify the contract documents, then where are the changes coming from (GC, Owner, subs?) and why do you need to track them? I think the answer to that last one might be the key. If you need to tie the changes back into the project record somehow, then by default they might actually change the CDs by changing the project record.
Are these for "record documents" or a "record BIM" that the Owner intends to use for FM? Why do you need a paper trail to document the changes if the model is correct?
One thing that jumped out at me right away was to use the Comment field in the Sync With Central dialog box to reference a change back to whatever piece of information was used to communicate/document the change. Those pieces of information should probably be kept track of outside of the project record (or in their own project record) depending on what the contractual arrangement for the services is.

Perhaps you could use the revision schedule with dates and a narrative of the change and why it was done. You don't have to tag the model, but you could.

Scott, I´m not sure that I completely understand what you´re trying to accomplish, but just maybe you´ll find this post by Martjin interesting ?

Here is the history to help understand the situation.

1. we were hired as the architect for this project a few years ago, we did the cd's in Revit but not as a "BIM" job. Just used revit to create 2d CD's. "model is only as good as the 2d drawings on the sheets" So for example walls aren't all the right height, etc. If you didn't see the problem in a view it didn't matter.
2. Owner has no clue what BIM is, finds out we used revit... Hires an owners rep who sells him on paying them to do BIM coordination during the construction phase.
3. Owners rep hires us to update the model monthly based on coordination needs.
4. so now we are issueing typical RFI's, etc from our model and going thru and "correcting" things like walls(mainly interior soffits and furring which don't get seen in many traditional views. so some of these changes change 2d views.

Its a nasty situation. Its like we are revealing all our mistakes, even though the 2d documents are pretty tight.

So it sounds like this guy talked the Owner into buying a Pinto and taking it to the race track. No offense intended there - Pintos are great for doing what they were intended for. If you want to race one though, you probably want to make some modifications.
So is there any specific contract language about the LOD entailed in doing "BIM coordination"? I would assume that it involves some level of clash detection and discipline coordination not included in your original scope?
It would seem prudent to ascertain what the Owner's specific and unambiguous expectations are for the BIM's intended use. Sounds nasty, but at least they didn't hire the GC to do this work. I would not classify what you are doing as finding "mistakes". You have simply been hired to bring the model up to a different LOD.
None of this really helps to answer your original question though. So if your scope is to update the model for this specific task (BIM coordination), what purpose does being able to track the changes through that process serve? If the project is going well (I hope it is), I don't think it would really matter unless in the course of the updating you find things that change the construction contract scope, schedule or budget. If that happens then the changes get pushed back and documented through the project record.