It will come as no surprise to some that I don’t think it was how they were “designed”. It’s how many 19th century flutes were made (for a range of historic reasons), and Irish players in the mid 20th century learned how best to deal with them. Not everybody can, but those who can can make them work very well indeed. So, the practical problem becomes can you learn how to do it?
Forget anything anyone says about “lipping up the note”. Nobody can lip a note that far. It’s all about getting rid of the low D entirely, shifting all the energy into the 2nd D and the higher harmonics. Any remaining low D content will make it sound flat.
The extraordinary thing is that, when we hear the harmonic series minus its fundamental (ie the rest of the harmonics but without the low D), we still imagine we hear the low D. And we interpret it as a very hard low D.
Interestingly, I’m having a bit of a play with a spectrum analyser while I’m typing this. And when I’m the most successful at “hardening” the Low D note and removing the Low D fundamental content, the bulk of the energy is ending up in the third harmonic, which is second octave A. But it continues to sound like a very hard D.
You might find it helpful “seeing” what you are doing. Here’s the URL for Tatsuaki Koroda’s Autotuner, which features a simple spectrum analyser as well as measuring the pitch.
http://www.shaku6.com/soft/s8tuner_e308.zip
In the Display pull down, select FFT Log 0-2700. Low D fundamental is just under 300Hz on the horizontal axis. The 2nd harmonic (2nd D) is the peak just under 600 Hz. Third harmonic (2nd octave A) is just under 900Hz (880Hz, or 440Hz x 2, to be precise). Try to minimise the first peak at 300Hz, and steer the energy into the others.
Then check the tuning.
The alternatives are, change the flute for one you can manage, or have the flute retuned. I’ve had to do a few over the years (mostly originals), but you should be able to find someone a lot closer than I am!