I've seen this mentioned a few times then stumbled upon this post and thought it'd be a good idea to spread this around. I'd also add to back up your SavedVariables.lua file on patch day before you run the game.
What it sounds like is that if you leave addons disabled and start the game, the data for those disabled addons will be lost. This is because of the way the data is stored now. Your pre-1.7 SV file will get parsed into separate per-addon data files. This is a good thing, but it means that on patch day, your addons all must be active so they can essentially tell the game their data must be stored. After that, you can re-disable addons and suffer no data loss.