Same, played Pluto Defense 25 Waves with Railjack, lost all Bonus Affinity.
Pluto Proxima Obol Crossing
directly first mission (wanted to lvl Nechramech)
3 Side Objectives done before Defense part, Mining + 2 necessary objectives to unlock the Defense (Hack Mod-Def + Hack Run around pew pew)
I played with Necramech most of the Mission, he Saryn.
We lost all Bonus Affinity back on Dry Dock (Orbiter and Restart changed nothing)
Confirmable No Bonus Affinity on Plexus, Necramech, Primary/Secondary Weapons and Warframe for both Client and Host