[LOGME] I'm actually not sure what that means myself and I've been using the program for three months. Now at this stage if you hit the folder for Part 2: Organisation and then look at the top of the to the tool bar's three buttons you can click the document button to change it to show one document ...
You more than likely don't have smart quotes turned off, because it's only deleting smart quote apostrophes. Thoroughly documented and logged bug. You can read more ON THIS THREAD including how to remedy it. Though a new beta should be out in a few days that fixes this.
The power was interrupted during an autosave, causing a corruption in your project file. Aka, your project.scriv file no longer matches the contents of your folders. There is a thread over on the bug forum about how to get your stuff back: Corrupt/Incompat Project Files
I need you to walk me through exactly what you did. I'm having a problem following what's going on with your process. Normally I bring in THE WHOLE FILE and then cut it inside Scrivener, is that what you did or are you copying in pieces at a time?