It doesn't really sound like sour crop to me. Not if they went on over a period of weeks. Their symptoms sound like a general decline in health that could be caused by various non specific things. If they went on into weeks then the stopping eating and only drinking may have led to their crops being squishy but there may have been an underlying problem and it might not have been sour crop.
When checking a chooks crop you need to do so in the morning before letting them out to feed. Overnight a chook should be able to disgest the contents of the crop so it should feel flatter (tho often not totally flat) and you should be able to gently feel around it and feel its is empty. If it has contents in, it will feel like either undigested food or if squishy you can then have a smell of the chooks breath and see if it smells nasty which would indicate sour crop.
If there is then a crop problem you would need to empty the crop properly (again, something I've written about at length elsewhere on the forum) holding the bird upside down and so on. Only when you have emptied the crop contents should you then try to give yogurt. TBH most birds will peck at it anyways once their crop is cleared out so worth letting them try on their own. If the sour crop or impacted crop has been going on more than a few days often medication is needed. I usually have had my chooks injected over the liquid in the dropper. Vet does this. As to if it then prevents it continuing or spreading and causing secondary infection elsewhere is really anyones guess. It depends on the bird really.
Regarding the windpipe, yes it may have done. Who knows, so don't beat yourself up about it. You need to be careful when syringing as it can go down the wrong way and not be nice for the chook. I'd always advise to either see it done and have it shown or read up carefully on it and which bit is which so you know where to aim.
I'd check your hens this evening once they have roosted and gently feel round their crop area. This will give you an idea of how their crops are before bedtime. Then in the morning before they eat or drink anything feel their crops again and see if they have digested their food. If they have then you can rule out there being a crop problem with any of your remaining birds and look at other areas of health.
Let us know how you get on with the crops tomorrow
