Lockdown is pretty forgiving. The eggs would have continued to develop during those 4 hours, so I would leave lockdown as is. If it's within a day, you're going to be just fine.
Rats have an even keener sense of smell than a dog and they can chew through nearly anything.
That shouldn't be a problem at all. Eggs get moved around by the hen all the time, so as long as you don't drop it you should be fine.
It depends on the style of the incubator, but stacking them may interfere with air flow and might affect the temperatures. I wouldn't do it, personally.
It's hard to find homes for extra males. I hope you find homes for them.
If you are willing to consider culling, have you considered something like these?
It's quite possible to get violence any time you have more than one male in the pen. In order to have more than one male you not only have to have a lot of space and hiding places, but they have to have the right personalities too.
Those injuries aren't bad at all. They'll heal up in a few days. It's good to separate them now, but if the boys can still see or hear the hens, you may end up with some that are completely scalped. They can and will heal from being scalped, but it's not pretty.
They're a bit young to be needing supplemental calcium. When they're adults, I would recommend offering the shell on the side and let them eat what they want.
Personally, I let them wander around in very shallow water until the poop balls fall off. It may take a few treatments to get it completely off.
As for the sand bath, I wouldn't give one to chicks under 3 weeks old. They're very good at finding creative ways to die, and eating sand instead...