It may of been that they weren't acclimated to the new temp/chemistry and they went into shock :( If they are in a 10g, they can stay there for another few weeks or longer, since there aren't as many.. so don't need to worry about moving them until they are bigger/stronger. The first month of their life they are at their fragilest.
A sponge filter would help.. get one of those valves that let you control the air flow from the pump to the filter.. just turn it on low and it will be fine. I've had mine set on low since they were free swimming with no problem. Yours should be fine as well.
The father should be able to take care of the fry with no trouble in there.. he won't have too many distractions, and possibly feel a bit more secure that nothing will try to harm them. BUT, he also may feel that the space is a bit too small and may try to cull a bit more. You will have to watch and see how he does. My male that was in the container was a first time daddy.. so I pulled him right after they were born because I was nervous.. but saw he had ended up having about 30 fry in his mouth when I transferred him and he started caring for the fry in his .33g keeper where I placed him to recoup. I did move the fry over though.. but he had built a nest and was watching them. A few ended up staying in there for about 5 days and he was still caring for them.. they eventually moved over too. So, you just don't know how the male will react until you watch them.. now I know this particular male is a great father, I can trust him with the fry for a longer period.
They will be small at 3 weeks - mine just hit the 2 week mark 2/3 days ago and they just got their pectorals and dorsals grown. So they take a while at first to grow. Once you are feeding them 2-3 times a day you will notice a difference quicker.
The ones that are left, if they seem to be fine, are darting/swimming around and exploring, looking for food.. basically active, then I would say they were the strong ones of the bunch and should make it.
Make sure to siphon 1-2x a day, both on the bottom to remove waste/dead food and top of the water for ammonia.. that will also help speed up the growth, as you will be removing toxins from the water and removing some of the growth stunting hormones they put out.
If this is your first spawn, I wouldn't beat yourself up too much.. this is one of those things where you learn as you go. A lot of breeders have lost easily two thirds of their first spawns because of making mistakes, etc. Now you know to breed them in the larger tank with a higher temp, or a tub in a tank, etc.. that way you can drip new water in continuously, they have more room to spread out and can stay there for 4-5 weeks before needing to go to a bigger grow out, can have the sponge filter ready in there, etc.
Not saying breeding in a small container/tank is a bad thing, I know a breeder who breeds exclusively in small bowls (I did it successfully too, but there were some negatives to it that made me not want to do it as much).. so it's possible, just have to find what works best for you and your fish, and find out how best to transfer them. Oldfishlady is a master at breeding, she would know how best to transfer such little ones - I'm too scared to move them when so young, so I don't know exactly how one would do it.