I guess I'll chime in here. I get the problem. I have the same problems sometimes as I would think most users do.
For example, I manage our CAD library and occasionally run across parts that were not modeled the way I/we would have liked in retrospect. Or we change the preference for where the base planes should be or we need to change a model due to an initial error, or another user snuck in his model to the library and didn't consider this stuff.
So before I decide to change it or not I do a where-used and decide if the number of assemblies affected and the number of instances of the part in those assemblies is worth the work required. Often the answer is no.
If the change would be helpful for future design but the WU count is too high sometimes I'll make the change but first change the original part name by adding "old" to the name. Insight handles the name change throughout the database.
But this is feasible for us largely because our products are one-off so we aren't that concerned with finished projects and so don't care if some of them have parts with old in the name. A downside is having obsolete files in the library. I could move them to obsolete so they're not visible to the users in the "good" library.
A better way to resolve mismatches would be great. Can it be done? Are there any CAD packages that do it well? Can development do it? The same issues occurred with SolidWorks.