Docking Archimedes Emerald on Phoenix Emerald in  

I got my favorite ship, the Constellation Phoenix Emerald and unfortunately, when you retrieve it, the regular Archimedes (not the Emerald one) is docked. I wanted to see if I could permanently equip the Archimedes Emerald to the Phoenix Emerald.
How to replace the stock P-72 Archimedes on the Constellation Phoenix with the Archimedes Emerald, plus a bug with the docking interface and a workaround for storing your phoenix.
I previously tried to land in a hangar, clipped into the hangar floor, exploded, and was respawned in the Nursa that was in the phoenix when it exploded. I was knocked out but couldn't respawn.
After this attempt I was able to dock and bed-log out, but couldn't make the docking interface go away even after logging back in hours later, and still couldn't land. That's when I decided to fly into a hangar, hover over the landing pad, drop the elevator, and go to the lobby. I then was able to store the ship.
Update:
I successfully cleared the docking interface and permanently stored the Archimedes Emerald on the Phoenix Emerald!
The bug that I ran into was that after docking the Archimedes Emerald on the Phoenix Emerald, the docking interface was still open, which prevented me from dropping the landing gear, and this required a workaround which took a while to figure out.
I tried:
Quantum traveling
Bed logging
Holding F to interact with the MFDs and in game controls
Logging out and in to a different server, then retriving the ship.
Steps to work around the bug:
1.) After docking, go into a hangar, hover low, exit with the elevator while the engines are still running, and store the ship.
2.) Swap guns and/or components, save the configuration, and reattach them, saving again (unconfirmed if this is necessary).
3.) To clear the docking HUD glitch, go to a space station, fly beside a pad, abandon the Phoenix, enter the space station, and claim the ship.
Sorry for the misinformation in the last iteration, I have been watching so many updates videos that it scrambled my brain. Title and thumbnail fixed on RU-vid