Version: minecolonies-1.12.2-0.9.127-ALPHA-universal.jar

I had most of my citizens disappear (3/4) and trying to recall them didn't work. When I did a /mc citizen respawn on my builder she came back but all her skills were down to 1. Is there a way to manually change her skills?

Nope, you need to get happiness higher to have higher spawn skills

i just checked and respawning does not reset it. Something else might've happened. We had an update which had that issue a while ago which has been fixed already. To level them up you can employ them in a library.