Company-A contributes code to Project-X under Apache License, and has patents on the technology contributed.
This is permitted [e.g. Citrix having patents related to CloudStack].
Company-B now downloads Project-X, and starts using it.
Due to business reasons, Company-B forks Project-X, and starts maintaining a private branch with private changes [which is permissible under Apache License].
Company-B is using the software commercially.
Is this a patent violation?
Note that there is no list of patents for Project-X maintained anywhere, and Company-B is not aware of Company-A patents which it may be infringing upon in private-fork of Project-X.