Do short circuits between transformer windings cause noticeable change in EMF?
You need to describe much more clearly what you are doing - what do you mean by transformer enclosure?

A shorted turn in a transformer radically affects its operation far more than just reducing the voltage because of the reduced number of turns.

The shorted turn acts as a shorted secondary so it will pass a high current in a normal transformer and cause it to burn out.

If you are measuring the inductance or EMF of a winding of a transformer it will cause both to go very low, almost zero because any EMF generated will be counteracted by the current in the shorted turn.