The basic principle of using magnets to move things is currently used in *every* electrical motor and generator on the power grid...
So, yes, you're right, it's an efficient system for -converting- energy.
However, I entreat you to think of your original question in a new way.
Take a large planetary body, such as Earth, does Earth lose its gravity when objects fall towards it? No... Why can't we use the gravity to create perpetual motion (or 'free energy')?
Anything that falls towards earth is losing PE and converting it to KE. Once the conversion is complete, the only way to make the object move again (by the same gravitational force) is to insert energy into the system by moving it to a new position where it has more PE.
The same basic principle is at work in your example. At some point in the design you're going to hit a point at which the system requires an input of energy greater than the energy 'generated' by the simple interaction.
Also, the force of the magnet attracts the objects towards one another, which balances itself out. In as simple terms as I can think of, while the metal might be moving towards the magnet, the magnet is being 'pushed' towards the metal with the same amount of force.
This means that in the entire system (magnet + metal), no work is actually being done (without an input of energy from outside sources).
The only reason we can easily think of situations whereeither the magnet moves and the metal doesn't (Fridge magnets), or the other way around (your example) is because outside forces working on the system (Gravity, friction, etc).