mention `gdk reconfigure`

Add note regarding the need to call `gdk reconfigure`
after changing values in `env.mk`

doc/howto/configuration.md

@@ -57,6 +57,9 @@ variable assignment is:
   copies of GDK, you should set `jaeger_server_enabled=false` in all but
   one GDK instance, and have traces get send to a single instance.
 
+If you change these files, make sure to call `gdk reconfigure` to ensure
+they are respected (e.g. that Jaeger is disabled).
+
 ### Example
 
 Here an example what `env.mk` might look like: