Removed command key, now it's flat, no spring, doesn't work

It's pretty easy to damage the keycap itself or the mechanism beneath it when removing these keycaps. My guess is that there is some damage that happened somewhere. Without high quality images of the parts involved it's difficult to make a recommendation since we have no way of knowing which part is damaged. One thing you can easily double-check though is that the little silicone nipple-like bump that normally sits directly below the keycap is present. Sometimes those come loose and when they do they can slide out of position or fall out which will cause the keycap to not sit correctly. If it turns out though that another component is damaged or some of the clips have become damaged, then you'll need to replace that component. Good luck!