I forgot to remove my mods. The game works fine, but some mods are still there and others are not. But now if I remove them, the 1.1 backups will be restored, which is not the best idea.
Remove all of your mods first. Reapply them if you want after installing 1.2.
EDIT:
Just fyi. After my 20 mins of playing, the one mod I did notice that was lost was the mod that adds BattleStations and SilentRunning buttons to all of the toolbars. They are now gone.
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