In general, these kinds of mass tag changes typically see some kind of run through on the Meta site first. That's one of the primary functions of retag-request when it is paired with discussion - to get voice on the subject of whether it's a good idea. This voice is ideally to come from both people who are familiar with the tagging system, and people who are familiar with the subject matter - the experts you suggest we consult. I think this practice should simply be continued.
If there is a big disagreement post-change, then what should be done depends on the nature of the change. If it's just renaming the tag, it's very easy to reverse and can be done almost instantly. So we just figure what needs to be the proper name, and once that's settled we make the change. I believe RPG went through a couple cycles with how they tag D&D, which was easier to handle thanks to it being renames.
If it's merged into another tag, though, then it's not easy to reverse. In this scenario, I think that before any further action is taken, everyone should discuss and lay down solid plans for how the tags should be in entirety - both involving the tag that was lost, the tag that it was merged into, and any associated tags. The goal of this would be not just to figure out what must be repaired, but also to prevent that kind of mistake from happening in the future.