It is highly recommended that you keep backups of your saves as you progress through the game. There are some issues with the game that can corrupt files sot that they are unusable. You will have to start all over in this case. But a simple backup can be a life saver.
That would be a freeze. Make sure your not running anything in the background if your computer isn't strong. The game takes a surprising amount of resources.
Hmm. It's a key item if I remember correctly. You talked to the middle guy right outside the big top, correct? Also, it doesn't work on those two plants when you first enter Route 2. It only works on the trees in the center of the route.
Just open the game in the episode 11 folder. You don't have to extract it into the episode 12. It'd probably break it. I think it can be fixed by redownloading as well.