So, right now I only have a bad answer.

The core issue is that RavenDB is, and I'm paraphrasing a little to make this more of a family friendly post, a pile. We need to rip it out of the product and replace it. However, currently we don't have the resources available to spend time on this free tool. So, the solution to the problem really is back to losing the history of your changes or dealing with RavenDB's size. 

Sorry about that.