You can run
godot --doctool <path> to dump the generated XML files. Running just
godot --doctool . will put them where they are supposed to be in the main /godot/ folder and will merge them in with the existing XML docs. In this scenario,
godot is the name of the path and name to your godot executable, for example
./bin/godot.x11.tools.64 would be a path from the godot directory root.
Note that this will regenerate the entire XML documentation. There is currently no way to individually update an XML file. This is because the scripting API used to all be in one XML file and was only separated into individual files during the 3.0 release. The command line interface has not been updated to reflect that change, so there is no way (as of yet) to update only a single file.