We use code that is part of this java library:
It reads the baseline, searches for the source fixlets in your environment, re-generates the baseline components and formats them so that for the most part Bigfix sees them as synchronized. There are some edge cases where Bigfix will still think they are not synchronized, but that is usually trivial formatting differences.
If you do end up using that library, feel free to open issues on it if you have problems synchronizing baselines.