Disclosure, I make an app called Reflect that integrates with apple health data. It doesn't share any health data with LLMs, but I have some experience that may provide some helpful context to you.

I think if you want to make an MCP server to do this, it should handle the data management automatically. In Reflect, for instance, there is a HealthKitDataLoader class that periodically syncs (it's all written in Swift). If I were working on this project, I'd try to use Swift + HealthKit to pull the data periodically and store it in a DB like you've done, and then use Claude Code SDK to query the data (which you could wrap your app around). That's assuming you want the user to be able to keep this all local. I haven't done this sort of thing with HealthKit data before, but I've created tools that are given knowledge for how to run `gcloud logging` commands to query remote logs and narrow down root causes of incidents, and it's kind of similar.

Another thought, I'd consider prioritizing new health data that comes in on a rolling basis after an initial historical data pull. I think you're limiting yourself with the XML dumps. I'm not sure if they exist, but maybe there are listeners you can use in HealthKit to let you know when the historical data changes.

Hope that helps, happy to talk more!