How does “Reputation” work?
Suppose I want to answer a question but I have commented the answer to someones post. So if I delete the comment will it deduct my reputation also?
No, comments don't have any impact on reputation. You don't gain reputation when they're upvoted and you don't lose any when they're deleted.
As comments don't earn you reputation, deleting them can't take any away.
The only thing that might happen is if another user decides that your answer was really a comment after all and decided to down vote it.