The controller is binding the values you pass in to a new Company entity. The new entity is not attached to the persistence context, it does not have the state of the pre-existing entity. When you save it JPA thinks you want to null out all the fields you don't have values for. 

Instead, you could have the controller bind its arguments to a DTO. Then in the service you look up the existing Customer, using findById, and copy the fields you want updated from the DTO to the entity. Then call saveAndFlush passing in the updated entity. 

It looks like there's an improvement over the DTO, you can use aJsonPatch to hold the updates passed in, see https://www.baeldung.com/spring-rest-json-patch
On the server the important thing is to look up the existing entity so that you have an entity that is attached to the persistence context and has all its fields current.