Hi, if you use the "SQL upgrade script package" your setting don't loses, follow the documentation
. But if they are settings from a plugin, you will surely have to update it as well and set it up again.
What I did was do a new installation up of my old version, copy the DataBase and over this to upgrade with scripts package. So i have my original configuration intact and can compare or pass settings.
Note: I upgraded from 4.0 to 4.1
I hope this was help!