This sounds a bit like someone else’s question but isn’t, really. Or at least I can’t find this very problem mentioned elsewhere; my apologies if it has been.
Having bought meself a new low D whistle to see if I’m up to the task (thus an inexpensive nickel-coated brass one), I found the hole coverage to be a minor problem (thanks to my big hands) and as a musician, associating the notes with the fingerings isn’t much of an issue.
However, after a few minutes of any given practice session, I began to lose the lower notes. Less than 20 min. after starting out each time, there was nothing to be had below C. I got either the higher octave or a noteless hiss. No amount of coaxing with airspeed, direction, or any mouth part from lip to soft palette seems to make any difference. It’s simply gone until I put it down for a couple hours. Then I have another few minutes of sound before it starts the vanishing act again.
The problem may not be what you are missing, but what you are gaining. Check to see if you are getting condensation on your whistle in the wndway or on the blade. Even a small amount of condensation on the blade mute your whistle.
The cure? People have said that coating the various affected surfaces with dishwashing liquid (and allowing it to dry) is helpful. I’m sure others will chip in on this.
I have played plenty of whistles that lose the lower octave for this very reason. Try soap or duponol to keep windway moisture down, and see if that helps you out. I’ve never used soap myself, so you’ll have to search the archives or ask someone who’s done it how to do it.
The moisture thing is probably the biggest culprit, but fatigue may be another. While learing the new wider finger spread for a low D, your hands may be tiring, even though you say you don’t have any problem reaching the holes. As a result, you may not be covering all of the holes completely. In the lower register, even a tiny leak can kill the note.
Well, no sooner do I get advice from all of the above (at amazing speed, I must say) than I’m sent off for a while. I’m back, and have tried the dishsoap idea, and it works like a charm. So nice to be able to play for more than 5 minutes at a time! At this rate I might even be a decent player eventually.
Make sure the blade is lined up with the finger holes. If the headjoint is twisted even a little, then you might not get proper finger coverage. However, sometimes the blade will appear to line up with the holes, but check to see if the fipple is also lined up with the blade. Oftentimes the fipple is not parallel to the blade. I have found this to be true on some whistles.
Otherwise, just keep practicing and your fingers will get stronger.
For an instant and ongoing remedy, just cover the top of the blow hole and blow through the whistle and shake it out - that always works for me to clear condensation whilst playing.
Stick your thumb over the fipple hole and blow like hell to dislodge moisture. The thumb isn’t strictly necessary, but it prevents deafness during this operation.