Right after Harith was sure Sara fell asleep, he went back out to do what he needed to do before locking her door from the inside, taking with him Sara's bunch of keys for various reasons.
First of all, he locked her door to prevent 'unwanted nuisance' from entering her room when she sleeps. By 'unwanted nuisance', he meant Lucas.
Second, he took her bunch of keys to stop Sara from leaving the building. No keys mean no entry to the Hall. Knowing Sara, she would search high and low for her keys before she would even step out of the house.
Logically speaking, how else would she lock the place without the keys? Putting in consideration that she might have left the last line of defence unguarded, causing not just hers but also her flatmates belongings at risk of being stolen.
Third and most selfish reason of them all, Harith needed the keys to be able to enter Bonington Hall freely. He chuckled as he felt victorious over such small matter.