Sounds like udev started discarding interface numbers from the firmware above a certain value as invalid. Considering that I doubt there are 16780032 onboard interfaces this sounds like a reasonable bug fix but an unfortunate change to find by surprise. Generally we avoid allowing such changes through when they are arbitrary default changes (upstream has changed how virtio devices are named a couple times now) so I think you should be safe with the new names. As an added protection you can copy 99-default.link to a new lower numbered file in /etc/systemd/network and remove onboard from the list to prevent the weird high-numbered names from reappearing. It will also work on older versions if you need to boot a system with an old version but want it to stick to the new name. The new name is derived from the PCI slot instead of firmware data which should be stable.
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Also, though, it's safer to just not ever match on the interface name. That's why systemd-networkd allows you to match on other things, like the MAC address.