I will be taking my son to visit my parents for a few days.
My parents live in the (European country) and my father receives disability benefits there hence the food they buy is bought from this money given by the government. The money the government gets is from taxes from businesses which includes alcohol bushinesses etc of which part of it is allocated to provided disability benefits and the like. My question is when I go to my parents place and eat from the food there, since the money is from a non Islamic government, would the food have a negative effect on the soul and if yes, how do I remove/control the effect?

No. It has no effects.