After the last patch, I have encountered this behaviour:
A character explores a location and encounters a henchmen.
After battling the henchmen (1st battle for a this-then-that henchmen), the game 'skips' with all discarded cards used having been removed from characters' hands but the henchmen not defeated and the character having the explore option (location deck has highlighted glow).
If the character explores, the henchmen is the top card but with all the discarded cards just used to defeat the henchmen gone, this is harder to win.
If the character wins this time, the game progresses just like you'd expect.