I think this is getting past the point that I can useful contribute further though I will note that the vast literature on the topic has dealt with this sort of issue in detail (though I don't know it well enough to comment in detail).

Saying that, I'll make one final contribution and then leave it at that: I suspect that you've misunderstood the idea of a rigid designator if you think it depends on the resolution at which you examine possible worlds. To say that something is a rigid designator is to say that it refers to the same thing in all possible worlds (note that this is a fact about language use). So to say that "water" rigidly denotes H2O is just to say that when we use the word water to refer to something in some possible world, we are talking about H2O. Issues of how precisely the details of the world are filled in are not relevant to this issue (for example, it doesn't matter what happens to the air molecules - this has no impact on the issue of rigid designation).

The point you raise is an interesting one about how we specify possible worlds but not, to my knowledge, one that's relevant to rigid designation. But beyond that I don't think I have anything more of use to contribute (simple because we've exhausted my meagre knowledge of the topic)...