The USPTO has a specific procedure for handling applications not under secrecy orders that interfere with applications under secrecy orders. According to MPEP 2306: "If an application not under a secrecy order has allowable claims that interfere with allowable claims of an application that is under a secrecy order, then the application that is not under the secrecy order should be passed to issue as a patent." This means that the USPTO will proceed with issuing the patent for the application not under a secrecy order. The MPEP further states: "An interference may be suggested with the application and the patent (unless the patent has expired) once the secrecy order has been lifted." This approach allows the USPTO to protect the confidentiality of the application under secrecy order while still allowing the non-confidential application to proceed to patent issuance. To learn more: Secrecy Order Interference Proceedings Patent Applications USPTO Procedures