1 Player hardcore
Here are my opinions for what they are worth.
I am assuming the Imperial player can not add or subtract defenders in between military and morphogentic attacks by the same Imperial units.
I'm unclear as to what you mean here. Could be it's sensible and I'm just easily confused.
I am also assuming the Imperium must include the Independent system unit if attacking its Independent Force(s) in the same sector.
Yes. All Independent Empire forces in the same sector (mobile & system) are included as defenders during an Imperial attack. 8.7.f
If the Independent empire home system is destroyed in the first round with mixed defenders (say invaders + rebels + the independent Empire) do the former Independent mobile units have to be included in the morphogentic attack against the other surviving chaos units?
8.2.b Imperial units may conduct a) military combat only, b) morphogenic combat only, or c) both military & morphogenic combat.
8.7.c Whenever there are 2 or more distinct Chaos Forces in the same sector, the Imperial forces may attack one, more, or none of them.
Based on that, I would say that if you chose to conduct both types of combat against all the mentioned types of Chaos Forces, then you would have to include the former surviving IE units in the morphogenic attack.
More importantly does the Independent Empire Leadership bonus apply for the morphogentic combat?
I'm not looking at the charts on the map right now, but if I recall correctly, the highest leader bonuses are always applied to combat results, whether military or morphogenic.
As a qualifier to my above statements I pulled those rule citations from the rules version posted on DG website. I think they were pre-release, but from everything I've read they look the same to me. There's a chance that something I cited is not identical to what is in the printed manual.