Ah, that's different!

When one changes metal shapes, one changes the resonant frequency of that shape. As a result, one can get some very unpleasant harmonics. Volvo had that with wind in the cabin if the rear windows were lowered on the V70's for example. It pounds with painfull force. Triumph got a noisy screechy ring going on some of their engines due to a resonance of the timing cover on some of their engines.

Luckily, the fix is usually quite easy. Change the frequency. Triumph stuck a blob of putty on the cover to dampen in. Volvo drivers don't lower the rear windows alone. You can do similar by a bit more hammering to change the shape, or relocating some components to the cut pieces and changing their resonance.

There is also the possibility that you've cut a structural shape, and have created a mechanical wiggle/shimmy as a result. I haven't seen your cuts and hammering, so I can't say. Rather unlikely, but possible.