Work on multi-level maps separately
 

I am trying to map a raid zone that has multiple levels in it. Because it is a current expansion dungeon, it is difficult for me to access a cleared version. I have nearly finished /loc collection for the first floor, and I have started /loc collection on the second floor. I want to begin line cleanup on the first floor and adding extra geometry like stairs, but I'm afraid if I add new lines to the first floor, or to any other floor, Mapper2 will overwrite all of the changes I've made. Do I need to finish /loc collection for the entire dungeon before I move on to the next step?

Think you need to make one set of locs for every floor, or it will be a mess.
You can always combine all the locs if needed.

I did separate the two floors with the `mapgroup` command, and I store the sanitized logs in different files. If nothing else, this helps my own sanity when trying to go back and add a missing line to one room. But don't I need to combine all of the log files into the same (layered) svg file, to make the layers line up properly? If I produce an svg for the first floor, cleanup the lines, and then add in the mapgroup for the second floor, won't the lines for the first floor also be regenerated?

You might be right there.
Think you need all the lines to line up as you said.
Combine all you log files with a mapgroup between levels should do the trick.
I don't rely remember, have not made a map in years :o
Hope the map guide can help you more.
But do please ask, we can always figure it out.