While I can't explain how it vanished I can suggest a few things to try to retrieve the project.
Base on the fact that projects (=applications) are managed in workspaces, and the studio (based on eclipse), can switch between them (via File>Switch Workspace), the crash may have caused an unintentional switch, or loss of workspace metadata.
So try to locate your workspace in the filesystem - a folder containing a .metadata subfolder, by default located in ~/workspace, and switch to it.
If the project does not appear, try to locate it in the filesystem (and note that a workspace may contain projects which are not physically located under it), and when you find it, import it via File>Import...>General>Existing Projects into Workspace).
If you found the project but for some reason am unable to import it into a workspace, you're welcome to zip it and send it to us for inspection.
Regarding the original problem of "Model Exception: Failed to create repository index", does that occur with any application or a specific one? If it occurs with a specific one, make sure that application can be launched as a regular web application, and if it does, try exporting it then (so that repository index building is separated from native export).
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