Bolt Cutters are found with a toolbox beside the Crimson Rover Shop. It is used to unlock certain areas blocked by chains, which are currently only the path to the Leaning Tower and the door to Blue Crystal Cave.
To the left of the front face of the Crimson Rover Shop are a few stacked crates. The Bolt Cutters are next to the crates. Press "E" to collect it.
Players will not lose their Bolt Cutters after they left the game, and unlocked areas will not be re-locked.