Put bluntly, your file structure is a mess. You appear to have nested multiple Scrivener projects inside each other. Difficulty compiling is the least of your worries: ALL of your data is very much at risk in this situation.
A normal project contains, inside the top level .scriv folder, the following items:
- The Project.scrivx file.
- A Files folder.
- A Settings folder.
- A Snapshots folder.
- Possibly a QuickLook folder, if it’s been shared with a Mac OS system.
- Possibly a Mobile folder, for iOS synchronization,
and NOTHING else.
Your Screenshot #1 has all of that, but it also has two anomalous .scrivx folders – itself a danger sign, as the master .scrivx document is a file, not a folder – and NINE .scriv folders.
This is a problem.
The second problem is that you are trying to save your .mobi file inside the project structure, which, as rdale pointed out, is a terrible idea. NOTHING should go in the .scriv folder except the internal contents of the project.
So, what to do about it?
First, backup everything using whatever third party backup tool you prefer.
Second, create a brand new folder somewhere like your desktop. Call it something like Recovered Projects. Create another one called something like Output Files.
Then, from the Scrivener Recent Projects menu, open your projects one at a time, confirm their contents, and use the Save As command to save a copy of each to the Recovered Projects folder. Close each project before opening the next. Use unique names so you can tell them apart. When you are done, the Recovered Projects folder should contain folders named “NewSOT Book Two.scriv,” “NewSOT Book Three.scriv,” and so on.
With Scrivener closed, browse to the Recovered Projects folder, open the NewSOT Book Two.scriv folder, and confirm that it contains a correctly formed project as described above. If it does, double-click on the .scrivx file to open it.
Now, Compile to .mobi format. Put the output document in the Output Files folder you created up above. Does that work correctly?