diff --git a/README.md b/README.md
index 01d45db..d279dfa 100644
--- a/README.md
+++ b/README.md
@@ -85,6 +85,7 @@ Make a PR similar to
 ```
 sed -i "s/41/42/g" *.repo comps-sync.py
 sed -i "s/releasever: 41/releasever: 42/" fedora-common-ostree.yaml
+sed -i "s/# - fedora-41/# - fedora-42/" fedora-*.yaml
 mv fedora-41.repo fedora-42.repo
 mv fedora-41-updates.repo fedora-42-updates.repo
 sed -i "s/42/42/g" README.md
@@ -95,9 +96,9 @@ sed -i "s/41/42/g" README.md
 
 ```
 rm fedora-rawhide.repo
-sed -i "/- fedora-rawhide/d" *.yaml
-sed -i "s/# - fedora-41/- fedora-41/" *.yaml
-sed -i "s/ref: fedora\/rawhide/ref: fedora\/41/" *.yaml
+sed -i "/- fedora-rawhide/d" fedora-*.yaml
+sed -i "s/# - fedora-41/- fedora-41/" fedora-*.yaml
+sed -i "s/ref: fedora\/rawhide/ref: fedora\/41/" fedora-*.yaml
 ```
 
 ## Historical references
diff --git a/fedora-base.yaml b/fedora-base.yaml
index 6a2c335..ef829f4 100644
--- a/fedora-base.yaml
+++ b/fedora-base.yaml
@@ -14,3 +14,9 @@ packages:
   # Portals for Flatpak
   - xdg-desktop-portal
   - xdg-desktop-portal-gtk
+
+# Kept in the leaf manifest as they are overwritten by Pungi in composes
+repos:
+  - fedora-rawhide
+  # - fedora-41
+  # - fedora-41-updates
diff --git a/fedora-cinnamon.yaml b/fedora-cinnamon.yaml
index 5df0893..ffa4c2b 100644
--- a/fedora-cinnamon.yaml
+++ b/fedora-cinnamon.yaml
@@ -10,3 +10,9 @@ packages:
   - xdg-desktop-portal-gtk
   # Include GUI to manage updates & Flatpaks
   - gnome-software
+
+# Kept in the leaf manifest as they are overwritten by Pungi in composes
+repos:
+  - fedora-rawhide
+  # - fedora-41
+  # - fedora-41-updates
diff --git a/fedora-common-ostree.yaml b/fedora-common-ostree.yaml
index efadd76..ac048a9 100644
--- a/fedora-common-ostree.yaml
+++ b/fedora-common-ostree.yaml
@@ -138,8 +138,3 @@ postprocess:
     ln -snf /usr/libexec/samba/cups_backend_smb /usr/lib/cups/backend/smb
 
 postprocess-script: "postprocess.sh"
-
-repos:
-  - fedora-rawhide
-  # - fedora-41
-  # - fedora-41-updates
diff --git a/fedora-deepin.yaml b/fedora-deepin.yaml
index 8bfa221..fbe280a 100644
--- a/fedora-deepin.yaml
+++ b/fedora-deepin.yaml
@@ -11,3 +11,9 @@ packages:
   - fedora-release-ostree-desktop
   # GUI to manage updates & Flatpaks
   - gnome-software
+
+# Kept in the leaf manifest as they are overwritten by Pungi in composes
+repos:
+  - fedora-rawhide
+  # - fedora-41
+  # - fedora-41-updates
diff --git a/fedora-kinoite.yaml b/fedora-kinoite.yaml
index 17b38cf..ae0adb8 100644
--- a/fedora-kinoite.yaml
+++ b/fedora-kinoite.yaml
@@ -45,3 +45,9 @@ postprocess:
 
     # Enable auto updates in Discover
     echo -e "[Global]\nUseUnattendedUpdates=true\n" > /etc/xdg/PlasmaDiscoverUpdates
+
+# Kept in the leaf manifest as they are overwritten by Pungi in composes
+repos:
+  - fedora-rawhide
+  # - fedora-41
+  # - fedora-41-updates
diff --git a/fedora-lazurite.yaml b/fedora-lazurite.yaml
index ed69623..623dee7 100644
--- a/fedora-lazurite.yaml
+++ b/fedora-lazurite.yaml
@@ -15,3 +15,9 @@ packages:
   - plasma-systemsettings
   # Portals for Flatpak
   - xdg-desktop-portal-kde
+
+# Kept in the leaf manifest as they are overwritten by Pungi in composes
+repos:
+  - fedora-rawhide
+  # - fedora-41
+  # - fedora-41-updates
diff --git a/fedora-mate.yaml b/fedora-mate.yaml
index 8eb0014..cbf4d46 100644
--- a/fedora-mate.yaml
+++ b/fedora-mate.yaml
@@ -13,3 +13,9 @@ packages:
 
 exclude-packages:
   - python3-unbound
+
+# Kept in the leaf manifest as they are overwritten by Pungi in composes
+repos:
+  - fedora-rawhide
+  # - fedora-41
+  # - fedora-41-updates
diff --git a/fedora-onyx.yaml b/fedora-onyx.yaml
index 3681ec5..f85be7e 100644
--- a/fedora-onyx.yaml
+++ b/fedora-onyx.yaml
@@ -12,3 +12,9 @@ exclude-packages:
   # Not needed in Budgie Desktop
   - tracker
   - tracker-miners
+
+# Kept in the leaf manifest as they are overwritten by Pungi in composes
+repos:
+  - fedora-rawhide
+  # - fedora-41
+  # - fedora-41-updates
diff --git a/fedora-sericea.yaml b/fedora-sericea.yaml
index 8044d24..48325de 100644
--- a/fedora-sericea.yaml
+++ b/fedora-sericea.yaml
@@ -18,3 +18,9 @@ exclude-packages:
   # nothing in the tree would use these
   - tracker
   - tracker-miners
+
+# Kept in the leaf manifest as they are overwritten by Pungi in composes
+repos:
+  - fedora-rawhide
+  # - fedora-41
+  # - fedora-41-updates
diff --git a/fedora-silverblue.yaml b/fedora-silverblue.yaml
index 20b8262..413372b 100644
--- a/fedora-silverblue.yaml
+++ b/fedora-silverblue.yaml
@@ -29,3 +29,9 @@ packages:
 exclude-packages:
   # Exclude GNOME Software's langpack plugin to avoid layering langpacks on Silverblue
   - gnome-software-fedora-langpacks
+
+# Kept in the leaf manifest as they are overwritten by Pungi in composes
+repos:
+  - fedora-rawhide
+  # - fedora-41
+  # - fedora-41-updates
diff --git a/fedora-vauxite.yaml b/fedora-vauxite.yaml
index e5f880c..3281a13 100644
--- a/fedora-vauxite.yaml
+++ b/fedora-vauxite.yaml
@@ -11,3 +11,9 @@ packages:
   - fedora-release-ostree-desktop
   # Portals for Flatpak
   - xdg-desktop-portal-gtk
+
+# Kept in the leaf manifest as they are overwritten by Pungi in composes
+repos:
+  - fedora-rawhide
+  # - fedora-41
+  # - fedora-41-updates