diff --git a/mpcdf_common.py b/mpcdf_common.py
index 19f61f0bc0f3dfdd5326e3957df42b9425ffca4e..9fb37c44990a27bb973dac86d0826a7f96d851ce 100644
--- a/mpcdf_common.py
+++ b/mpcdf_common.py
@@ -839,8 +839,16 @@ Macros:
     new_prj = ElementTree.tostring(root, encoding=osc.core.ET_ENCODING)
 
     for name in sorted(prjconf_repos.keys()):
-        prjconf_ours.extend(prjconf_repos[name])
+        if name not in old_repos:
+            prjconf_ours.extend(prjconf_repos[name])
+            prjconf_ours.append("")
+
+    if not remove_old:
+        prjconf_ours.append("# Obsolete repos: ")
         prjconf_ours.append("")
+        for name in sorted(old_repos):
+            prjconf_ours.extend(prjconf_repos[name])
+            prjconf_ours.append("")
 
     prjconf_ours.append(prjconf_end_marker)