The game saves system state, such as config options, text you've read, and whether you've completed the story, only when it exits normally, so if it crashes, it loses that state. Since it checks whether you've completed it once as one of the conditions for making the secret ending available, you won't be able to access that at this point.

You shouldn't need to worry too much. As long as you have a save near the end, or at least after connecting the Fragments, it's just a matter of loading it up and skipping until the end; if you change the option to skip all, then you can use the "skip" button at the start of each chapter that you need to go through, and go do something else while it works through that. After you get the regular ending and return to the main menu, close the game, so the state is saved.

If you don't have a save after connecting fragments, it may not be too big a deal. Connecting Fragments in the proper order is something you can do before finishing the first time and still get the secret ending without doing it again. Just do it in the proper order now, and make a save right before you go to the last Fragment that leads to the third act. When you reload the save, the secret ending should be there.