Damian, I’m a newbie, but will offer my thoughts on this! If you haven’t seen the TeamRecorder youtubes, I’d really suggest you look at them – Sarah Jaffrey gives lots of good tips on technique.
More specific info is needed to understand why you can’t play the lower notes. Most likely, it’s because you’re not covering one of the holes completely, and it could be any hole, even on the left hand. Sarah J. suggests playing note by note to uncover the culprit.
Another reason could be that you are blowing the low notes too hard. Generally, you need to reduce breath pressure on those.
It could be related to small hands or a disability in reaching those keys. I started out playing an Alto Ecodear and really had issues reaching those low holes. In my case, I am developing stiffness due to arthritis and a serious bike injury, plus, my rt. pinky is crooked in the wrong direction. I tried stretching exercises, etc., but decided it wasn’t worth it. I just can’t get ergonomically comfortable playing the alto. So I switched to soprano and am alot happier!
I have Yamaha YRA 312b, The lowest notes require much less pressure than the notes just above. They also pop up easily into a harmonic if you use too much pressure or attack. The harmonic will be clean, though. If the sound is squeaky and pitiful, more likely a leaky finger.
I will echo previous post about watching Sarah on Team Recorder showing how to diagnose this.