If you have a 1000kva transformer than can you work on that transformer?

No. From what you're saying you're taking the input to the 2kV transformer in a microwave and replacing it with a 1MW input. The transformer will burn in milliseconds of power.

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The installation and maintenance of a 1000 KVA transformer can be worked on in a de energized state. To do so live could be extremely dangerous at any voltage.