[Nush]

It's quite normal for them to make a nest in their wheel after a cage clean. I wouldn't disturb his new nest because that's where he feels safe. I'm guessing it's the noise of the food rattling that scares your hamster. He will eventually get used to it even though it is awful to see him jump every time. But they get used to noise gradually. Eventually he will realise it's better to sleep in a proper nest and he'd move.

My hamster does the same but he doesn't seem to be deterred that he has a food store and nest in his wheel when he runs in it. The food and substrate goes everywhere!

May be next cage clean don't change too much of the bedding . Lift the nest if you can (it should be easier to do this if you use a lot of tissue paper as bedding) and clean the bottom of the cage and gentle place the nest back.