By default, when changing the information in the Orbits settings, it affects both the calculation of the satellite position and the navigation message. In other words, there is nothing special to do to have the ephemeris and almanac updated accordingly. With the introduction of data sets in version 21.11, it might not be the case. For example, starting with 21.11, you can have different data sets for ephemeris, almanac and the orbit calculation. Take a look at this post for more details.
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