Don't give your initial resume (fake) to the HR. Give them the original one. I don't know about how your company hiring process goes, but in mine, they called all the previous companies and asked them about me.

If your manager is asking you to submit your resume directly to the HR, then give them your original one without worry. If he is asking to give it to himself, then talk with him about your situation.

I am saying this from experience. Same thing happened to me and I talked with my manager, who helped me a lot.