Regarding "a Windows 10 server environment," I am not clear what you are referring to since there is no Windows 10 server operating system.
The issue of mapped drives being interrupted with Group Policy updates isn't unique to Esri or file geodatabases, although ArcGIS doesn't handle them well at all. I believe the issue started popping up more after Windows 8.1 was released.
The organization I work for encountered large impacts from this issue when it stood up Citrix virtualization in a new data center environment. The solution we applied was to change the GP from "replace" to "update."
Group Policy is quite flexible, most of the time. We have applied the "update" change to specific virtual machines used by Citrix in our data center. We chose machine-level mapping because all users on the machines will want to see the same behavior, but I believe the GPO can be handled at a user level as well. Anyone who says it can only be applied globally either doesn't understand the question or doesn't understand Group Policy.