diff --git a/mender-convert-modify b/mender-convert-modify
index cebd93a..7d8c2d5 100755
--- a/mender-convert-modify
+++ b/mender-convert-modify
@@ -169,10 +169,14 @@ EOF
   # functionality, but lets get rid of them to avoid confusion.
   #
   # There is no Mender integration for EFI boot or systemd-boot.
-  sudo rm -rf work/boot/loader
+  sudo rm -rf work/boot/loader work/rootfs/boot/loader
   sudo rm -rf work/boot/EFI/Linux
   sudo rm -rf work/boot/EFI/systemd
   sudo rm -rf work/boot/NvVars
+  for empty_dir in $(cd work/boot; find . -maxdepth 1 -type d -empty); do
+      sudo rmdir work/boot/$empty_dir
+      sudo rm work/rootfs/boot/$empty_dir
+  done
 
   log_info "Installing GRUB"
 
diff --git a/scripts/bootstrap-rootfs-overlay-demo-server.sh b/scripts/bootstrap-rootfs-overlay-demo-server.sh
index b608c20..59e1967 100755
--- a/scripts/bootstrap-rootfs-overlay-demo-server.sh
+++ b/scripts/bootstrap-rootfs-overlay-demo-server.sh
@@ -52,7 +52,7 @@ if [ -z "${server_ip}" ]; then
   exit 1
 fi
 
-sudo chown -R $(id -u).$(id -g) ${output_dir}
+[ -e ${output_dir} ] && sudo chown -R $(id -u).$(id -g) ${output_dir}
 mkdir -p ${output_dir}/etc/mender
 cat <<- EOF > ${output_dir}/etc/mender/mender.conf
 {
diff --git a/scripts/bootstrap-rootfs-overlay-hosted-server.sh b/scripts/bootstrap-rootfs-overlay-hosted-server.sh
index e73c514..e7abd1e 100755
--- a/scripts/bootstrap-rootfs-overlay-hosted-server.sh
+++ b/scripts/bootstrap-rootfs-overlay-hosted-server.sh
@@ -53,7 +53,7 @@ if [ -z "${tenant_token}" ]; then
   exit 1
 fi
 
-sudo chown -R $(id -u).$(id -g) ${output_dir}
+[ -e ${output_dir} ] && sudo chown -R $(id -u).$(id -g) ${output_dir}
 mkdir -p ${output_dir}/etc/mender
 cat <<- EOF > ${output_dir}/etc/mender/mender.conf
 {
diff --git a/scripts/bootstrap-rootfs-overlay-production-server.sh b/scripts/bootstrap-rootfs-overlay-production-server.sh
index ef70c8d..e0f868f 100755
--- a/scripts/bootstrap-rootfs-overlay-production-server.sh
+++ b/scripts/bootstrap-rootfs-overlay-production-server.sh
@@ -57,7 +57,7 @@ if [ -z "${server_url}" ]; then
   exit 1
 fi
 
-sudo chown -R $(id -u).$(id -g) ${output_dir}
+[ -e ${output_dir} ] && sudo chown -R $(id -u).$(id -g) ${output_dir}
 mkdir -p ${output_dir}/etc/mender
 cat <<- EOF > ${output_dir}/etc/mender/mender.conf
 {