From a normal daily calorie expenditure only a fraction goes on physical movement. The greatest share goes on cell biochemistry, followed by digestion, then normal stuff like heart beats. Additionally all the physical movement like rolling over when you sleep and reaching for a coffee. This means that for most people an hour work out will add less than 10% to your daily energy expenditure. And your body can naturally reallocate energy from different processes if you are in deficit. Like running some other things in a slightly lower energy mode.

If you are in a serious deficit for a long time it can be harmful. But the more immediate worry is getting the right things at the right times.