I am using SDK 14.2 with nrf52840 board. In my project I am using USB and BLE together. I have noticed that when I enable the LE Secure pairing and after that my USB driver stopped giving me APP_USBD_CDC_ACM_USER_EVT_RX_DONE even though I am sending data from the PC to the Nordic chip. This issue is intermittent and doesn't happen all the time. I am using micro-ecc backend for crypto operations for LE Secure pairing. If I use the Legacy pairing , I don't see the issue.
Within a coulpe of weeks, a new version of the SDK that fixes quite a few bugs will be released. I would recommend you to wait for that release, and then try again.
Also, which version of the nRF52840 do you have? Make sure to have the latest version.