Go to
(whatever drive you've got the games on)\Users\(whateveryourusernameis)\AppData\Local\Google\Chrome(or other browser used to play the flash version)\User Data\Default\Pepper Data\Shockwave Flash\WritableRoot\#SharedObjects\(a string of numbers and letters)/chat.kongregate.com/#orava/mutilate
therein you should find three files: settings.sol, items.sol and menus.sol. Copy or cut them, these are the files from the flash version.

Then go to
(whatever drive you've got the games) on\Users\(whateveryourusernameis)\AppData\Roaming\games.rava.mutilate\Local Store\#SharedObjects\#orava\mutilate
and paste the files, overwriting the ones in this folder if needed.

You should not have the game open while doing this, as it may overwrite the files you paste into the folder after you close it requiring you to do the process again.
It should all work as soon as you start the game.
I suggest the application "Everything", to more easily find the needed folders, though you can very well do it manually.
You might need to enable "view hidden items" from the file explorer menu in order to find some of the folders required for the process.