In Windows, with some NICs, especially Intel, Windows may enable features on the card that break it in Linux. It is hard to troubleshoot as what you'll see is that the NIC is still detected in Linux, the NIC/port will be up but nothing will work (eg. DHCP requests or even static IPs won't work). You may see STP bridge traffic but that is all.
In a corporate environment this can result in many calls to support and is essentially downtime and an unnecessary waste of resources.
Generally these are any of the "Wake on LAN" or "Wake on Magic" or simiilarly named features. Make sure you disable those under Device Manager for any of your NICs.
The quick fix for this (if you don't have control over Windows) is powering off the machine and powering back.
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