Two things:
1. I'd greatly appreciate it if you could share that datasource. Is this the one in the official repository?
2. I largely agree with your point that it's not always obvious when a datasource change or update is going to cause data loss - a pain I've experienced a few too many times. Even when updating official datasources, it's a risk due to the custom applies-to functions we might be using. It would be great if there was at least some logic that allowed the import of a datasource, but allowing the administrator to choose to override the applies-to function or not. Or maybe even (for advanced users) make manual changes to the XML doc before importing to prevent datapoint renaming.