Save file location from the FAQ:
[quote]PC:
C:\Users(your name)\Saved Games\Pokemon Insurgence (or whatever appropriate game you’re playing)
If you are on Windows XP and cannot locate the above folder, the folder should just be the folder with your Game.exe and the rest of the files.
Mac:
Right click the app, Show Package Contents, drive_c, Program Files, Pokemon Insurgence (or whatever appropriate game you’re playing)
In both cases, it is the Game.rxdata file. You can create backups of it, or copy and paste it to a different computer to continue your game.[/quote]
Like Kuzunoha said, if you’re on windows(you’ll have to confirm the location if you’re on XP), you can download the core and not worry about your progress. If you’re on a Mac, you’ll need to move your save(s) over from your old core to your new one(which has also been mentioned in the download post 
).
Though I’m curious why just copying, replacing and merging some files or folders caused your computer to crash.
Edit: Could you expand upon what you were doing before the crash?