Reducing transformer lamination thickness
If I understand you correctly you want to increase the window area so you can fit more windings in the transformer.  You want to do this by removing some of the laminations?

If so, with all else the same you are going to increase the flux swing, increase the core losses, and reduce the thermal mass.  If the transformer was designed for 200kva and you run the modified transformer at the same power, best case it will run hotter with less margin.

Worse case it will trip its thermal protection and shut down.

Worst case it has no thermal protection and fails spectacularly.

However it sounds like you are changing the windings as well.  Without knowing exactly what you are changing and how, and what the intended use and power requirement is it's impossible to say what the effect would be.