if you don't receive your EWS certificate in time for GATE counseling, your category will automatically change from GEN-EWS to GEN, meaning you will be considered under the General category during seat allocation.

It is safer to apply as EWS category to get reservation quota because at the time of counselling the respected authority will ask you to represent your income certificate so first apply for income certificate then EWS even if you haven't received the certificate yet, to avoid any last-minute issues and ensure you are considered for the appropriate seats.

THe only consequence is they will degrade you to general category thats it