diff --git a/pkg/config-reader/update.go b/pkg/config-reader/update.go
index 69467eead..b6a3b16d0 100644
--- a/pkg/config-reader/update.go
+++ b/pkg/config-reader/update.go
@@ -63,11 +63,15 @@ func (r *ConfigReaderImpl) readImportsToUpdate(configFilePath string, cfg *aqua.
 		sort.Strings(filePaths)
 		for _, filePath := range filePaths {
 			subCfg := &aqua.Config{}
-			if err := r.Read(filePath, subCfg); err != nil {
+			subCfgs, err := r.ReadToUpdate(filePath, subCfg)
+			if err != nil {
 				return nil, err
 			}
 			subCfg.Registries = cfg.Registries
 			cfgs[filePath] = subCfg
+			for k, subCfg := range subCfgs {
+				cfgs[k] = subCfg
+			}
 		}
 	}
 	cfg.Packages = pkgs
diff --git a/pkg/config-reader/update_test.go b/pkg/config-reader/update_test.go
index 48f529215..de4b12a4c 100644
--- a/pkg/config-reader/update_test.go
+++ b/pkg/config-reader/update_test.go
@@ -137,10 +137,10 @@ packages:
 				t.Fatal("error must be returned")
 			}
 			if diff := cmp.Diff(d.cfg, cfg); diff != "" {
-				t.Fatal(diff)
+				t.Fatal("cfg:", diff)
 			}
 			if diff := cmp.Diff(d.cfgs, cfgs); diff != "" {
-				t.Fatal(diff)
+				t.Fatal("cfgs:", diff)
 			}
 		})
 	}
diff --git a/pkg/controller/update/registry.go b/pkg/controller/update/registry.go
index 53784dc1f..0bc3f69f7 100644
--- a/pkg/controller/update/registry.go
+++ b/pkg/controller/update/registry.go
@@ -30,6 +30,10 @@ func (c *Controller) updateRegistries(ctx context.Context, logE *logrus.Entry, c
 	for _, rgst := range cfg.Registries {
 		if commitHashPattern.MatchString(rgst.Ref) {
 			// Skip updating commit hashes
+			logE.WithFields(logrus.Fields{
+				"registry_name":    rgst.Name,
+				"registry_version": rgst.Ref,
+			}).Debug("skip a registry whose version is a commit hash")
 			continue
 		}
 		newVersion, err := c.newRegistryVersion(ctx, logE, rgst)