Just Cause 2 lost game
Solution 1:
Did the auto save function kick in during the "new game"? If so I'm afraid its lost.
The way saved games are handled in Just Cause 2 is that you are expected to save regularly to ensure progress isn't lost. The auto save only takes up one "slot" and is rewritten frequently.
It's actually more of a safety net against random deaths or errors than a long term way to save your game.
Solution 2:
You should always save your game manually trough the menu, so whenever you start a new game and your auto-save file is overwritten, you will be able to load it back up using one of your 10(or so) custom save slots.
For those on the pc: The save files are located in your documents folder under the name 'square enix/just cause 2/', you might get previous versions back from there if windows automatically saves recent states of that folder.
Good luck re-doing stuff.
though 36 hours isn't much time lost relatively speaking, it took me about 60 hours of gameplay to finish ALL locations AND challenges.
Solution 3:
I am afraid that there is not much that can be done.