Infiltration and combat

I’m running a 5e campaign, and our group is going into a period of the campaign that will likely involve a lot of ‘sneak in sneak out’ encounters/series of encounters, like assassination missions or thievery.

The problem is, I’m not sure how to keep it balanced with the so-called ‘adventuring day’; it seems like if they plan it well, or even if they don’t, they should have at most two fights in a row, and those in very quick succession, because they can hardly sneak in, have two fights in a row, rest for an hour (!!) without being caught, and then have two more.

How can I fit infiltration-style encounters or quests into the combat framework of D&D 5e?

(NB: I’m afraid the system is more or less non-negotiable; there’s a pandemic, and even if there weren’t, we’re a good few levels into the campaign; it just wouldn’t work to change up systems.)