Kerbal Space Program

Here is what I initially did and here is how I worked around the bug.

here is essentially what I had on the spacecraft from top to bottom

1. Nose Cone
2. Upside down fairing
3. Upside down docking port
4. right side up docking port
5. Lander Can
6. Science bits
7. Upper Stage with lander legs
8. Lower Stage

Now, I did not want to take the whole fairing module with me to Duna and had planned to dock this descent stage with a ferry stage already in orbit (hence the docking port). Therefore I tried mounting the fairing upside down and figured I would undock and therefore decouple it and the nose cone while in orbit.

Unfortunately, when in orbit after I ejected the fairing (before undocking the docking ports), the craft thought that it was landed and was moving on the ground. The orbit disappeared from map mode but the craft did not change its velocity. I was able to reorient the craft using SAS, however when attempting to timewarp or head back to KSC I was unable to because the craft was moving on the ground.

I was able to remedy this issue on the next launch by getting rid of the top part and just placing the fairing mounting bracket below the science bits right side up. It meant that I will need to carry it with me all the way to duna and back, but it resolved the issue.