1st question: In this scenario, the villain runs to hide at another open location. When you defeat him at location 'A', set aside the villain, location 'A' is immediately closed and you draw 1 blessing card from the box. Mix up the villain and the blessing, then randomly select one of the 2 cards for location 'B', the other for location 'C'. Then, you move on to explore the remaining locations. The villain will run like above if you encounter him again with 2 open locations OR if you encounter and defeat him at the only open location, you win.
2nd question: No, cards don't have memories, so partially wounded monsters/henchman/villains are shiny and new when you meet them again.
@DrJay is right.
When you defeat a Villain that location is immediately closed (you have no choice).
The Villain then runs to an open location, randomised by taking blessings from the box.
If you fail to defeat a Villain, they still run (they do not just shuffle back into their own deck) but this time you take blessings from the timer deck and include the first location (which is not closed) in the randomisation.
Have a read through "Encountering a villain" on p18 of the rulebook for more details.