Any User Defined Reports metadata, including folders, is in (for Windows, as an example) %APPDATA%\SQL Developer\UserReports.xml.
I tried to simulate your scenario on 3.2.2 by ...
1. Running ...\bin\sqldeveloper.exe from a Windows command line console.
2. Creating a dummy folder and copying a report into it.
3. Issuing a Ctrl+C from the command line to terminate the application.
After that, checking the UserReports.xml, all those changes were saved despite the abrupt termination. Not sure why yours either did not get saved or, at a minimum, are not getting displayed in the Reports View. Can you see them in UserReports.xml? If you add a new folder, then exit and restart the product, is the folder saved? Also, more detailed information on your environment (OS, JDK version, use of something like Citrix, use of more than one instance of SQL Developer at the same time, etc) may give us additional clues.
SQL Developer Team
OK, apparently using Ctrl+C does not guarantee that the JVM terminates immediately, as we can read about here...
Therefore my test could not simulate what you suffered when SQL Developer "shut down unexpectidely". If the reports / folders do not appear in the UserReports.xml, probably they are lost and gone forever. Especially since the SQL History view does not pick up the queries run from the Reports view.
However if you prototyped / ran any of the queries in a worksheet before copying the code to a report, you may be in luck as that goes into the SQL History. In addition, if you had added this line at the end of your sqldeveloper.conf file
your Logging view would have one or more lines referencing the SQL queries ran from the Reports view.
Going forward, I would check the following:
1. Make sure you can successful save folders and reports to UserReports.xml.
2. If not, perhaps your user settings got corrupted.
3. Backup your connections (specifically, Export these), UserReports.xml, etc., before deleting or renaming the system3.2.20.09.87 folder.
4. When you restart SQL Developer, you must decide whether or not to migrate prior settings.
5. Also it never hurts to upgrade to the latest JDK 1.6.0_xx if you stay with SQL Developer 3.2.2, or 1.7.0_xx if upgrading to 4.0.2.
Hope this helps,