In a one-way parent-to-child replica, running the replica schema commands removes a feature class from the child replica list if the feature classes in the child geodatabase are unregistered as versioned.
The issue can be reproduced with a full model, but not a simple model. With a simple model, the layer is not removed. With the full model, versioning is required as support for a full model sync requires it. In this case, users should use a simple model as it was designed to support unversioned data on the child.