What is worse, in your opinion: a) Leaving a minor plot point unresolved, or b) resolving it in a way that comes off like an afterthought? I won't go into detail, but in the romantic suspense novel I'm licking into shape, I throw threat after danger after threat at my MCs, until finally they survive The Biggest Threat of All. Whew! I then proceed to resolve the personal growth issues and the love story in a way pleasing to them both, and write "The End." The other day, however, I realized I'd forgotten about another Potential Really Big Threat I'd introduced earlier in the story. My MCs are sure to bring it to mind at some point: they aren't stupid, and neither are readers. But I can't have it be anything more than potential without its highjacking my whole denouement. So. after giving my MCs one last big scare, I have it turn out that the Potential Really Big Threat has always been contained--- literally--- and nobody has ever had anything to worry about. It feels perverse, doing it that way! Like I'm poking the reader with an electric cattle prod and saying, "No! You can't relax now! I have to get you frightened for my characters one more time! Though--- ha-ha!--- it's really nothing at all!" And it hurts my pride. Here I'd thought I had all the plot strands so nicely tied up. Phooey.
Afterthought plot things are gross. If you forgot about this Potential Really Big Threat, how important could it be? Can you get away with cutting it completely? If so, it'd save you work of weaving it through the entire story and it'd save readers confusion.
I feel like I was there. I vote with @Imaginarily, but, how many Potential Really Big Threats are there? I mean, I'm on my way to work and I hit traffic. Instead of sitting, I turn left. More traffic, so I turn right. More traffic, so I turn left again. Turns out one of those traffic jams was just a red light, and I could have been on my merry way if I'd just waited a minute. But at a certain point I'm only (over) reacting to what's in front of me. In a suspense novel with enough dangers, I'll be forgiving if one of those dangers was only perceived.
I'd definitely try to rework things to include this potential threat. Revealing at the eleventh hour that it was never a big deal would seem like a bit of a cop out to me, unless maybe it's lampshaded - point out (like Samurai Jack said) that it was probably inevitable that at least ONE of these seemingly big deals was a bust, have a laugh, and move on with the actual plot. Otherwise, I'd cut it, because an unfulfilling plot resolution is worse than no plot to resolve, IMO.
If you can eliminate it earlier, I think that'd be my vote, because neither of the options you presented seem all that appealing to me. Alternatively, could you work in the resolution of that threat before you resolve the real big threat? And maybe include it as a contributor to the real big threat? Like, while the team were distracted with false threat A, they weren't paying enough attention to real threat B, and then they resolve A but then yikes, right away get hit with B?
Can it be clear to the reader, but not the MCs, right from the start that it isn't a real threat? I suppose that only works if you have another POV character, or if you can somehow show your POV misunderstanding something in a way that the reader knows it's a misunderstanding but the character doesn't... tricky. I have a similar issue. I just don't have the page space to give all the little sub-plots extensive tying up, so some of them just have to get wrapped up in a paragraph or two. They're necessary to progress the plot but their resolution isn't that important to the story. In my situation, I haven't found a better way of doing it.