I suspect this really simple, and a matter of user error, but if I mute one of two instruments, they both are muted; if I hit solo in the Mixer, both instruments play. Is it possible that both instruments are on the same channel? They are the same instrument. I haven’t done anything with channel assignments, just loaded them from the Halion Se library.
If this is in a score that you created in a version prior to 1.1 then there was a bug in the initialisation of the mute/solo data. If you do Play → Apply Default Template then this will reset the engine data and the mute/solo should work as expected.