everyone, including his friends, assumes Maverick has been obliterated
by the attack. They become disheartened, believing their comrade has
been lost forever.
However, unbeknownst to them and to the readers, Maverick manages to
miraculously survive the assault. Unveiling a surprise twist a few
chapters later, Maverick makes a triumphant comeback.
Fool your characters, not your readers
There's an old saying you can fool some of the people part of the time, but you can't fool all of them.... Your readers are a diverse group. Accept that some are never going to be fooled by a main character's fake death, mid-story.
This trope has been over-used – I can think of probably a dozen Star Trek episodes where a main character is obliterated into subatomic matter by an energy force that would incinerate half a planet, only for them to be fine (barely an inconvenience) by the end of the episode.
Unfortunately, this means people are expecting it, you can't rely on the reader being surprised. Worst-case: you can't rely on readers' suspension of disbelief because you're setting up a situation where the reader will doubt the author (because they have seen this trope in so many instances) and then be proven correct.
Readers know how this works: no corpse = not really dead.
When the reader predicts the plot in spite of the author's attempt to hide it, it's deal-breaker.
Use your Ensemble
In the absence of your hero/leader, the ensemble becomes your main character. They can't all sit around feeling sad, there is still a super-villain on the loose who is pretty sure he can now do whatever he wants unimpeded.
And he's right!
You have a ticking clock: the super-villain is strong enough to defeat any of them individually. They MUST work together, but their established patterns are no longer working. Some of the team will recognize this and want to re-group, while some of the team want revenge. Without a clear leader, schisms emerge that pull the group in different directions.
Ultimately, they will make decisions in-line with their individual characters, rather than trusting in the group. Your ensemble/team experiences a negative arc. For example, a hot-head rushes in to fight putting another member in jeopardy, and a third member decides unilaterally to abort the mission and get them out of there, ruining the agreed plan.
Cue: villain laughing maniacally because even he didn't predict how well this would work!
Make the stakes clear. The ensemble is not a team without their leader. Everyone feeling sad because a friend died is not a story conflict –– however, members of the team starting to feel like they're better off on their own is a major crisis that can break-up the team forever.
This incident has consequences that impacts each member of the group. Interpersonal dynamics that were held in check are now uncertain. Someone will attempt to assume command, others will reject them or find their leadership skills lacking. Mistakes are made, doubts are sewn, and dysfunction grows. No one likes losing, this is salt in the wound.
How each character deals with this shifting dynamic is far more interesting than a technobabble deus ex machina. As a rule, plot contrivances that help the protagonist are rejected (like a physics loophole where the MC is blipped into another dimension miraculously unharmed).... But plot contrivances that generate conflict and hurt the protagonist are accepted.
Keep the reader engaged in the unfolding drama. Your goal is to exploit the current conflict happening right now. This is not a sad, low-point in the story, this is a crisis that is getting worse. Make your ensemble suffer, make them react in ways they'll regret, let them make mistakes that bring danger on the others.
You have enough cast members to create a diversity of opinions and reactions. Their initial thoughts are not 'Oh no, what about the team?' Rather their initial actions suggest they believe the team is still functional. It's when they try to implement a plan, they learn the group is failing – after they have put themselves in danger. A defeat will be reason enough to loose faith.
That one character who won't let go...
It's fine for Tom to observe there is no corpse, and believe his 'Dad' can be brought back. By saying so openly, you deflate readers who are looking to outsmart the author. There is still a mystery for Tom to solve, but it's not 'what happened?' it's more 'what's Tom going to do about it?'
Tom has never been without Mav, and you only need 1 other character to say Tom is in denial and refusing to accept the inevitable. This isn't just a physics puzzle for Tom – although that may be the way he's been trained to deal with problems. It's potentially a defining crisis for Tom's identity – does he even have a purpose without Mav...?
Even if Mav is somehow alive, Tom has no means to bring him back. The rest of the group will have different levels of sympathy for Tom, but eventually agree their resources are better served fighting the villain. Tom will have to choose whether his loyalty to Mav outweighs his need for the group, perhaps giving him insight into what the others are going through.
Choose the bigger payoff
In short, you have a chance to remove a key component of your group and let the reader experience the team failing as a consequence –– a situation that has a lot more story potential than just a fake-out death.
This is a chance to get to know your characters, individualize their motives and manners, and show how they can be on the same side and still disagree. While they are not amateurs, they are under extreme pressure and against the odds. Even if they were functional the task would be hard. It doesn't need to be anyone's fault, just the natural clashes in their nature when their diversity begins to work against them.
You also have a chance to allow members to review their commitment without Mav holding them together and assuring their wins. Along with the team experiencing a negative arc, you need the individuals to experience their own arcs: how they relate to each other and the group as a whole, what they are contributing and how they have been taking advantage. They need to recommit (to the cause, if not the group) before entering their final battle against the villain.
Treat this incident as a crisis that disrupts the team, but ultimately makes them stronger. It would be nice if they can learn something about themselves and each other (character growth) –– more than just Mav is a 'chosen one' who comes back like Ass-Kicking Jesus to save the day. With a stronger team, you have the option of bringing back Mav at less than full strength (even gasp vulnerable after his ordeal).
Heroes that cannot be defeated are derided as 'Mary Sues' wearing 'plot armor' who are always saved by 'deus ex machina' (intervention from the author). But readers get invested in characters who face uncertain challenges, and (hopefully) choose to do the right thing despite personal risks.