diff --git a/libraries/entropy/db/skel.py b/libraries/entropy/db/skel.py
index f521f5167..39d404ddf 100644
--- a/libraries/entropy/db/skel.py
+++ b/libraries/entropy/db/skel.py
@@ -4419,6 +4419,10 @@ class EntropyRepositoryBase(TextInterface, EntropyRepositoryPluginStore):
                 # mark it as disabled if it's not available
                 if en_use not in pkguse:
                     pkguse.add(use)
+            else:
+                # for compatibility reasons with older Entropy versions,
+                # use flags not in pkguse are considered disabled.
+                pkguse.add(use)
             disabled_use.add(use)
 
         enabled_not_satisfied = enabled_use - pkguse