I have two main projects that I am using with Scrivener.
In the first one I had two folders (entire chapters) disappear when I was rearranging them. I clicked and dragged with the mouse and when I let go to move the folder it disappeared completely! Then later when I went to compile both of those folders were there and were giving me a double chapter. I figured out how to unclick them so that they wouldn’t be included in the compile but I still cannot find them anywhere. They are not visible and I have looked everywhere that I can see.
In the second project I had my entire first chapter disappear on it’s own. It’s gone and I didn’t touch it. I tried getting it back through the zip file that I saved as a backup. Even though that was the only option that scrivener gave me for backing up scrivener would not open it. This is especially frustrating because I have no other backup and that chapter is just completely lost.
For the first one, with the double chapters, it sounds like the folders just got moved to be children of another item. If you click into the binder and then choose View > Outline > Expand All, that will reveal all the levels in the binder and you may find it then. If you know the names of the folders or some specific text in them, you could also try finding them via the Project Search in the toolbar. When you run the search, the binder will switch to show the Search Results collection; then you can select an item and choose View > Reveal in Binder to switch back to the standard binder and see that item in context.
Scrivener cannot open ZIP files directly. To access a zipped backup, copy it from the backup folder to the desktop, then either right-click the backup and choose “Extract All” or double-click the folder to open it and drag out the enclosed project folder to extract it. If you decide you want to replace your current working version with the backup, make sure both copies are closed in Scrivener, then delete or rename the original (e.g. from “MyNovel.scriv” to “MyNovelBAD.scriv”) and move the extracted backup copy to your preferred location (e.g your user Documents folder). You’ll need to open it again in Scrivener by double-clicking the “project” file or using File > Open in Scrivener before it will appear on your Recent Projects list.