At the moment #include works by reading the config on the file:

This breaks #ref that are in another file "higher" up in the include hierarchy, ex:

(aero.core/read-config (clojure.java.io/resource "config_test.edn"))
;; =>
{:a "AAA"
 :b "AAA"
 :c {:d nil} ;; nil here - should be "AAA"
 }

;; config_test.edn
{:a "AAA"
 :b #ref [:a] ;; OK
 :c #include "config_include.edn"
 }

;;config_include.edn 
{:d #ref [:a]} ;; this is not resolved

Without knowing too much about aero's internals, it seems a possible solution would be to include .edn files without resolving the tags at the 'include level.