I think it's fine to add paper bedding and then when you "spot clean" you'll gradually remove more and more of the wood shavings and add more and more paper bedding. Then at the next substrate change you can replace most of it. Alternatively you could change it all in one go, but then the bedding won't have the hamster's scent and it may bother the hamster a bit. However, providing you don't clean anything else at the same time or remove the nest and hoard, it is an option to just switch it all over in one go
You could keep a little bit of the wood shavings back from the top, and spread that on top of the new bedding, so it still smells familiar. Those bits can be spot cleaned out as and when, later.
So there isn't a right or wrong way to do it and some might depend on the hamster's personality. If it's a particularly skitty hamster then it might be better to do it gradually.
