If you're playing single player in BF3, you're doing it wrong. It's horrid.
Anyhoo, that happens to me every bloody time I turn the game on. Cloud and HDD are both corrupted. Just set up your classes and they should stay the way you want them. You will have to change your controls and server filter every time, unfortunately.
Ew, BF3 single player
So all of my stuff is still there? It says I can create a new save, but that it'll overwrite everything once it autosaves. So far, I've just decided not to create a new save so that I can keep all of my stuff. Unfortunately, that means that I can't unlock anything else ever again until I decide to actually create a new save.
If I do create a new save, does that mean I lose all of my unlocked weapons and stuff? Or do I get to keep my blood, sweat, tears, and a couple days worth of effort?
You don't lose any of your weapons or unlocks, those are attached to your Gamer Tag. You can continue unlocking items as you rank up and get kills as those are tracked on Battlelog by EA.
If you create a new save, you probably just have to redo your customizations. Again, your weapons and unlocks are attached to your Gamer Tag so they'll be fine.