Veeraj,

No it wouldn't affect  your engineering option entry. Just make sure you enter the options for Karnataka NEET UG counselling through the relevant link. For your reference, given below is the link of option entry and KEA NEET UG Counselling Portal.

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Karnataka Medical/Dental NEET UG Option Entry

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Karnataka NEET UG Counselling Official Portal

Hope it helps.

Good Luck.