Hi Lili
Sorry to hear you are STILL going through such a hard time with this.
I know there is a lot of controversy over soy but so much of it is misunderstood or NOT understood yet. Yes, some research says that large amounts of phytoestrogens may not be good, but there is also research and clinical studies that show it's not bad at all. There is nothing conclusive at this point in time and for every bad you can find a good, so at this point, for me I don't even consider it an issue. I would not expect a toddler to take to Nutramigen at this stage in the game - you might want to ask her if she will prescribe toddler Neocate, although TBH I am pretty shocked she would react so strongly to the soy issue but not have a clue that Nutramigen wouldn't exactly go down a treat

There are flavoured Neocate versions meant for toddlers and it might be worth calling her and asking if she can get you a script for one to try, if she's against soy.
On the toilet training front, I am only going to share what is my own opinion and I totally recognize that not everyone feels this way so am not offended if you and others disagree with me (and thus with that please keep in mind that I don't mean if offenseively either) - but I reallly think it is a bad time to start training. Early toilet training at 8-9 months or so and you can end up with a child who is ready now, but starting a boy at 21 months, I think it is asking for more stress than you need at this time. Sure there are those who DO get it and it works but unless he is really showing signs of being ready and it's going to happen in 2-3 days, then I would leave it. I've always read that boys are closer to 3ish before they are ready to do a train, unless you are looking to spend the next 3-4 months working at it - and so with this soft poo problem, IMO, I would just give it up and wait 6 months. But that's just me

If soy has never affected him before, I would find it a bit strange that it suddenly started to affect him. Usually, as you know, intolerances are grown out of not into, though nothing is impossible. With it being summer is he having more fruit? Have you tried cutting him down to just the bare minimum and seeing if he is better?
To trial milk, what has your dietician suggested? I cracked one night and gave DS a slice of cheese: we had just moved to Germany and I was struggling reading labels in German, because even though the basic words (milch, butter, jogurt) are similar it was thinks like "partially separated casein" and so on that I was worried about, kwim? So after the cheese he was fine, so I did three or four days in a row where I gave him 5ml of milk in a syringe and he was fine. There were a few days of some icky poops but we were told by the hospital paed in England that runny poops were normal for ALL kids when moving onto cow's milk. And after a few days he was fine, so we've not looked back.
I am also curious when you say he is threatened with failure to thrive - what have they said about this? If this is the case then I would expect the dietician to do a bit more than tell you to put him on a milk that he's never in H going to drink. She should be offering you more support with his diet including ways of fattening him up and piling on some calories. Kwim? The other thing is, 10.7 kg at 21 months is FINE so what is their problem? He is on the 9th percentile so it's not even close to FTT at this point unless he is losing weight or was on a much higher percentile than he is now? It's more than my DS weighed at 21 months and not too much less than what he weighs now at 24 months (he's just crossed the line to 11kgs)!! Anyway, I would still go back to your dietician and ask them how they can help you to help him pile on some weight if that is what they are wanting from you/him.
Has she given you any advice on when to do a milk challenge? At St Helen's they will often do one at 12 months and one at 24 months if needed (ie/ not outgrown at 12 months) so you shouldn't be too long before they will do a trial for you.
I also think you are right with the mood issues - it is SO hard to tell if it is just him/his age/toddlerhood or if it is the food but if you feel in your gut that it is worse on days with lots of soy you are probably right. I just can't think of why it would be fine before you took him off of the soy and then suddenly appear when you put him back on it.

Have you done any reading/searching on that? Just to see what you come up with.
I"ll have a think and a read and see if I can come up with anything for you - in the mean time if i were you I would ring the dietician and ask for at least a phone consultation appt on how to fatten him up and asking if you can get flavoured neocate (actually even your GP will prob be able to write the script for that as they should have the dietician's summary letter by now...).
hugs Lil, i know you've been through a lot with this xxx