I will refer to the Player's Guide, page 85 the block on the left.
while fatigue and stress generally come and go quickly in
encounter mode, GMs are encouraged to limit the recovery
of fatigue and stress in story mode.
And if you read this PDF on page 71 there's a whole paragraph explaining recharge in story mode. But here's a quote :
As a rule of thumb, each time the scene shifts or an event occurs
in story mode, each player should remove one recharge token
from each of his recharging actions, talents, conditions, or other
recharging cards. Within a given scene or challenge, one “round”
can roughly equate to enough time for each player to have a chance
to act or respond, after which each player may remove one recharge
token from each of his recharging cards.
So from those two readings we can conclude that you should roleplay the effects of Fatigue and Stress and if you spend the talent card during the story mode to remove 2 stress or fatigue.
For instance everybody is exhausted from climbing that mountain all day but one player cheer up the troop and say: "Cmon folks! Only a couple steps and we'll be able to make a camp!" He use the talent card on the party sheet and the party move forward and ignore the effect of fatigue until they reach a nice spot to establish the camp.
There's also an action card called Assess the situation that let you recover fatigue or stress. Roleplay this one appropriately. If you stop for a breather (about 5 min) and the action as a recharge of 2, just let them recharge this card once per scene or a set period of time it make sense. Taking a 10 min breather won't let you fully recover from a whole day of climbing.
Recovering stress is about the same. Make sure people participate in the roleplay of recovering stress. If you are in story mode and want to vent off some stress using the Assess the situation: "Let's go to the tavern and have a drink. Let's talk about what's bothering ya. Ask for an ale and remember you are the best dwarf in town man!". Drinking the whole night might let you recover stress but next morning, give one of fatigue for the hard night.