diff --git a/sdk_container/src/third_party/coreos-overlay/.github/workflows/docker-apply-patch.sh b/sdk_container/src/third_party/coreos-overlay/.github/workflows/docker-apply-patch.sh
index 6fb563fa83..2591579fb0 100755
--- a/sdk_container/src/third_party/coreos-overlay/.github/workflows/docker-apply-patch.sh
+++ b/sdk_container/src/third_party/coreos-overlay/.github/workflows/docker-apply-patch.sh
@@ -4,7 +4,10 @@ set -euo pipefail
 
 branch="docker-${VERSION_NEW}"
 
-pushd ~/flatcar-sdk/src/third_party/coreos-overlay || exit
+git -C ~/flatcar-sdk/src/scripts checkout -B "${BASE_BRANCH}" "github/${BASE_BRANCH}"
+git -C ~/flatcar-sdk/src/third_party/portage-stable checkout -B "${BASE_BRANCH}" "github/${BASE_BRANCH}"
+
+pushd ~/flatcar-sdk/src/third_party/coreos-overlay >/dev/null || exit
 git checkout -B "${branch}" "github/${BASE_BRANCH}"
 
 VERSION_OLD=$(sed -n "s/^DIST docker-\([0-9]*.[0-9]*.[0-9]*\).*/\1/p" app-emulation/docker/Manifest | sort -ruV | head -n1)
diff --git a/sdk_container/src/third_party/coreos-overlay/.github/workflows/go-apply-patch.sh b/sdk_container/src/third_party/coreos-overlay/.github/workflows/go-apply-patch.sh
index 3e6b3cefa3..12cf6af095 100755
--- a/sdk_container/src/third_party/coreos-overlay/.github/workflows/go-apply-patch.sh
+++ b/sdk_container/src/third_party/coreos-overlay/.github/workflows/go-apply-patch.sh
@@ -4,7 +4,10 @@ set -euo pipefail
 
 branch="go-${VERSION_NEW}"
 
-pushd ~/flatcar-sdk/src/third_party/coreos-overlay || exit
+git -C ~/flatcar-sdk/src/scripts checkout -B "${BASE_BRANCH}" "github/${BASE_BRANCH}"
+git -C ~/flatcar-sdk/src/third_party/portage-stable checkout -B "${BASE_BRANCH}" "github/${BASE_BRANCH}"
+
+pushd ~/flatcar-sdk/src/third_party/coreos-overlay >/dev/null || exit
 git checkout -B "${branch}" "github/${BASE_BRANCH}"
 
 versionOld=$(sed -n "s/^DIST go\(${GO_VERSION}.[0-9]*\).*/\1/p" dev-lang/go/Manifest | sort -ruV | head -n1)
diff --git a/sdk_container/src/third_party/coreos-overlay/.github/workflows/kernel-apply-patch.sh b/sdk_container/src/third_party/coreos-overlay/.github/workflows/kernel-apply-patch.sh
index b4c68a54c5..47e28e29b6 100755
--- a/sdk_container/src/third_party/coreos-overlay/.github/workflows/kernel-apply-patch.sh
+++ b/sdk_container/src/third_party/coreos-overlay/.github/workflows/kernel-apply-patch.sh
@@ -4,7 +4,10 @@ set -euo pipefail
 
 branch="linux-${VERSION_NEW}"
 
-pushd ~/flatcar-sdk/src/third_party/coreos-overlay || exit
+git -C ~/flatcar-sdk/src/scripts checkout -B "${BASE_BRANCH}" "github/${BASE_BRANCH}"
+git -C ~/flatcar-sdk/src/third_party/portage-stable checkout -B "${BASE_BRANCH}" "github/${BASE_BRANCH}"
+
+pushd ~/flatcar-sdk/src/third_party/coreos-overlay >/dev/null || exit
 git checkout -B "${branch}" "github/${BASE_BRANCH}"
 
 versionOld=$(sed -n "s/^DIST patch-\(${KERNEL_VERSION}.[0-9]*\).*/\1/p" sys-kernel/coreos-sources/Manifest)
diff --git a/sdk_container/src/third_party/coreos-overlay/.github/workflows/runc-apply-patch.sh b/sdk_container/src/third_party/coreos-overlay/.github/workflows/runc-apply-patch.sh
index 333ac621fb..28ee335f2a 100755
--- a/sdk_container/src/third_party/coreos-overlay/.github/workflows/runc-apply-patch.sh
+++ b/sdk_container/src/third_party/coreos-overlay/.github/workflows/runc-apply-patch.sh
@@ -4,7 +4,10 @@ set -euo pipefail
 
 branch="runc-${VERSION_NEW}"
 
-pushd ~/flatcar-sdk/src/third_party/coreos-overlay || exit
+git -C ~/flatcar-sdk/src/scripts checkout -B "${BASE_BRANCH}" "github/${BASE_BRANCH}"
+git -C ~/flatcar-sdk/src/third_party/portage-stable checkout -B "${BASE_BRANCH}" "github/${BASE_BRANCH}"
+
+pushd ~/flatcar-sdk/src/third_party/coreos-overlay >/dev/null || exit
 git checkout -B "${branch}" "github/${BASE_BRANCH}"
 
 # Get the original runc version, including official releases and rc versions.