It's fine to leave them on manual. I suspect the issue was with the IP ranges and firmware. With PnP, provided the cameras are not activated, the NVR will handle adding and configuring the cameras automatically when you connect them directly into the PoE ports. It's hard to pinpoint why the cameras lost their links after the firmware upgrade. I'd lean toward your NVR firmware running V3.4.101_180904 and that you may not have had DHCP enabled. Glad you came right in the end.