It depends on how the magazine was modified, but the most common way of modifying magazines is to install a pin. I'm using the word “pin” very large. It could be a pop rivet. It could be an actual pin, or it could be a screw that's welded in. There are a variety of ways of putting in what would amount to a pin.
They are relatively easy to remove. They can be simply drilled out, and the magazine in most cases will function normally at that point. The hole on the side of the magazine does not impair its operation.