I noticed today (when I was checking version compatibility) that this plugin will revert back to the original id if you de-activate/activate it (which is perhaps what you mean by “updated”?).
It now (as of version 0.4) no longer cleans up after itself by removing settings on deactivation. Instead, all settings should just live in the database permanently, which is probably preferable for most users. That said, users should ALWAYS check to make sure their amazon associate id is correct after updating or activating. Let me know if you have any further problems.