Rejected for promotion based on one missing metric. Due to some conflicts, I didn't get to work on a project which would have helped me bridge the gap.
Getting rejected multiple times is not a bad thing in itself, but what's important is why your packet was rejected.
You're in the 2nd category, so you should ensure that you call out this area of improvement, and what you've tried to do (even if you weren't able to work on the ideal project)
If your manager's cool with it, then you should just let them do it. This is a good sign IMHO as this shows that your manager's willing to fight for you.
What happens if I am rejected second time? Would it affect future promotion cycles?
I don't know for sure as I'm not a VP of Engineering at your company, but I would be really surprised if this hurts you. Getting rejected for promotion happens all the time. I know engineers who were rejected 3+ times before finally getting it (this is very common at Amazon with SDE 2s).
I have helped many engineers get promoted, and when I create growth plans for them, I always tell them that it's more of a guideline than a strict checklist. While you missed one of the goals, it's possible that you crushed the other goals so hard that you deserve the promotion.
Best of luck!