One of the mods stated they didn't want defender synergies to be a complete surprise to attackers because of what they can do to affect abilities, but Kabam wasn't sure how to address This. Well, guys, you already have a system in place for this sorta thing you can extend.
What happens if you place MODOK, Void, Sentry, Morningstar, Mephisto on defense? By their question mark icon, you sometimes see this guy:

I don't always see it, but I have every now and then. Maybe it only shows up if there is a charge active, like one added through a synergy!
So what's the way to show synergies? Add a similar icon to the champ, either on the small [ ? ] thumbnail in the map, or as part of the champ info - which is mostly hidden - available when selecting your attacker for a battle.
The icon can have additional info via color coding. For example, if the champ receives a boost from someone else (Stark receiving one from Green Goblin) make it blue. If they're receiving a synergy through their own pairings (Stark receiving a synergy from Vulture or Iron Man) then make the icon green. Is it a two-way synergy (Daredevil and Black Widow)? Make it purple. Does the champ benefit from two
other defenders forming a global team synergy (entire team gains +6% health, etc)? Make it yellow. Do they have all they all three, or some other combination of potential synergy scenarios? Spin the color wheel. Or just use a number representing how many synergies have been applied to the one champ either through specific or global circumstances.
Or do none of that, just add the icon, let us try and figure it out ourself (like so much other content) and we'll at least have synergies in war again.
DONE! Now we know a synergy is active. If you choose to add color coding, we know 1. there is a champ feeding this one, so who could THAT guy be and/or B. the synergy is limited to who the champ looks for alone. This doesn't exactly give away the hidden defenders, either. How exactly are you going to narrow down one of Carnage's synergies with the spider-family? You really, really can't with great ease.