Update. Device came back after 2 reboots, so maybe I have some failing hardware.
dmesg while device was missing:
pci0: <ACPI PCI bus> on pcib0
pcib1: <ACPI PCI-PCI bridge> irq 16 at device 1.0 on pci0
pci1: <ACPI PCI bus> on pcib1
pcib2: <ACPI PCI-PCI bridge> irq 16 at device 1.1 on pci0
pci2: <ACPI PCI bus> on pcib2
dmesg after 2 reboots:
pci0: <ACPI PCI bus> on pcib0
pcib1: <ACPI PCI-PCI bridge> irq 16 at device 1.0 on pci0
pci1: <ACPI PCI bus> on pcib1
ix0: <Intel(R) PRO/10GbE PCI-Express Network Driver, Version - 3.2.12-k> port 0xe020-0xe03f mem 0xf7d80000-0xf7dfffff,0xf7e04000-0xf7e07fff irq 16 at device 0.0 on pci1
ix0: Using MSI-X interrupts with 9 vectors
ix0: Ethernet address: 00:1b:21:cd:a1:0c
ix0: PCI Express Bus: Speed 5.0GT/s Width x8
ix1: <Intel(R) PRO/10GbE PCI-Express Network Driver, Version - 3.2.12-k> port 0xe000-0xe01f mem 0xf7d00000-0xf7d7ffff,0xf7e00000-0xf7e03fff irq 17 at device 0.1 on pci1
ix1: Using MSI-X interrupts with 9 vectors
ix1: Ethernet address: 00:1b:21:cd:a1:0d
ix1: PCI Express Bus: Speed 5.0GT/s Width x8
pcib2: <ACPI PCI-PCI bridge> irq 16 at device 1.1 on pci0
pci2: <ACPI PCI bus> on pcib2