I have a potential partial solution to the docking port version of the root part problem.
Pre-1.11, I built a Mun Mining lander with the intent to refine the ore in orbit, so I had a tank and drills with no converter (and a docking port on the top and side). I realized later this was foolish with almost no net fuel (or net negative), so launched a Converter 125 with docking ports on either end and attached it to my lander (four parts, "lower" port-converter-battery-"upper" port). Now I could fill my fuel tanks before leaving the surface with a load of ore (where I had a 250 converter in orbit), and the "upper" converter port became my default docking port.
With 1.11, I decided to make this a permanent feature, and ran into the docking port problem. The "upper" converter docking port was now my root part, and while I could undock the converter stack and disassemble everything from "lower" end, I now had a floating docking port I could not get rid of and would rather not throw away.
Thanks to you, I figured out the root part was my problem.
I decided to try and force a change to the root part by undocking and redocking. This was my procedure:
Lander docked to space station by "side" lander port, the troublesome "upper" converter port hanging off the end.
Undock lander from station
Undock "lower" converter port from "upper" lander port, converter module now floating.
Dock "upper" lander port and "upper" converter port (basically flip converter upside down)
Dock "side" lander port to the same station docking port
At this point, the old "lower" converter port was hanging off the station and I began to disassemble the stack. However, this forced a change in the root part of the converter stack, so now I could not only disassemble the "lower" port and the converter, but now the "upper" converter port was no longer the root part and I could also take it off.
At the moment, I cannot complete the entire retrofit I had planned, as the "upper" lander port is still the root part for the lander itself and I want to rearrange the parts beneath. However, I will keep trying this trick and see if I can also shift the root part of the lander proper: I may have gotten lucky with the converter.
I don't play with mods or DLC, so anyone should be able to try this out and see if you can replicate it or if I got lucky. If your spacecraft only has one docking port, I'd add another and force the "new" port to become the root part so you can retrofit the spacecraft (I expect I'll have to do this for a couple space station modules).
I'll report back as I continue to test this out on other spacecraft. I intended to make several docking port changes to my existing stations and landers (replacing normal size with large, adding large, etc.), so I should have quite a few testing candidates.
