You probably know this but just in case, Rinex doesn't contain ephemeris data, but the Trimble native (.t02 and similar) do.
Therefore, if the Leica data was taken at a significantly different time than the Trimble data I would suspect that you don't have an orbit for the missing data. Simple fix is to go the internet download and download the missing files. You will be able to get the broadcast and rapid orbits, but might not get final orbits unless the data is about 2 weeks old. Depending on the source it also may not include all the constellations.
It has been several years since I did any static GNSS processing, but I think that MGEX is the place to get it now. When I transitioned to a different role, IGS was pretty dated, but maybe they have added stuff. Also, keep an eye on the time frame, if the data spans over month or 2, you'll probably want to do separate downloads for each session or blocks of sessions, but if it is all in about a month or less, just let it download orbits for the whole time frame.