For any modders out there, my Override and Portraits folders didn't get altered in any way. Still make a backup, but you should be safe if you didn't remember to.
I actually found out this the hard way when working on my Eve of War mod. I updated the release candidate build and I thought I had backed up the last thing I had worked on. Turns out I hadn't moved the rar file I had it in into another folder so thats probably a few hours work gone. So this is very good advice
My BG/SOD didn't start at first. I had been fiddling around with BGEE.lua to register my portraits and the game wouldn't start until I removed that file from override. I tried exporting the current BGEE.lua, but it won't run even with the new one in override.
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EDIT: Pressing F5 fixed it.