Haha, religion can have that effect on people. They come back eventually, Maybe I was just being impatient, it seems like it might just take a lot longer for them to travel than it says it will on the map.
I figured out the equipment reassigning thing, it is a bit tedious, but it does seem to work. I definitely remember who my hammer dwarves are at this point.
I'm having another problem. So my first mission was a raid and I sent both of my squads, and they both went. The next two missions I sent them on were raze missions. For both of the raze missions only one of my squads would go, and it was the same squad that wouldn't leave both times. The squad members that wouldn't leave had their jobs listed as something along the lines of: can't access site. They would just stand around doing nothing but occasionally going to satisfying needs (saw some purple prayers and socialization). I gave the squad a move order and canceled it, then they went about their normal businesses and were removed from the mission.
All my nobles positions are filled, and there is a noble leading every squad. I currently have my pop cap at 105, could that be part of the issue? Can I only send out one squad to raze a site if my pop cap is that low? My militia commander is in the squad that wont leave, does that have something to do with it? I am pretty sure I've sent my militia commanders out plenty of times in other forts. So strange, has anyone else experienced this? This is the first time I've had this problem, and the first time I've played with a custom pop cap, so I'm a bit suspicious it has something to do with that.