A thousand apologies for how disgustingly long it's taken, but the 5.7 and 5.8 Fuck Global Warming builds now have a new feature that you can turn on in the settings that compares an opened file to the previous import (if that data is available), and should sort of give you what you wanted, in that it should only touch brushes and entities that have changed.
Unfortunately, I spent so long working on this in bits and pieces that I... completely forgot your original ask was mesh only, which would need... Another Layer on top of this.
I'll see about getting you a 2.7a version that should hopefully not take quite this long to appear, altho it's... quite a tricky proposition, given how everything fits together, so I hope this at least gets you somewhere.