You can tell I am not the expert on running FoundationDB, as I think I gave you bad advice with my previous reply.
The actual answer is to create a symbolic link. So for instance you can have a directory that has folders for all the different versions of FoundationDB, and then make a “Current” folder which links to the latest one. The configuration file will use the “Current” folder. When you want to switch versions, you can change the symbolic link to a new folder.
If the server restarts for other reasons it would prematurely switch to the new version. For patch releases the new version is allowed to communicate with the old version, so the database will continue operating as usual. For major/minor version upgrades, the when the new version attempt to talk to the old version its communications will be rejected. It is equivalent to that process being down until the upgrade is finished.