diff --git a/build/common.sh b/build/common.sh
index 80c6fc7d8a3..2db1fae3226 100755
--- a/build/common.sh
+++ b/build/common.sh
@@ -654,7 +654,6 @@ function kube::build::stop_rsyncd_container() {
 function kube::build::rsync {
   local -a rsync_opts=(
     --archive
-    --prune-empty-dirs
     --password-file="${LOCAL_OUTPUT_BUILD_CONTEXT}/rsyncd.password"
   )
   if (( ${KUBE_VERBOSE} >= 6 )); then
@@ -679,16 +678,19 @@ function kube::build::sync_to_container() {
   # directory and generated files. The '- /' filter prevents rsync
   # from trying to set the uid/gid/perms on the root of the sync tree.
   # As an exception, we need to sync generated files in staging/, because
-  # they will not be re-generated by 'make'.
+  # they will not be re-generated by 'make'. Note that the 'H' filtered files
+  # are hidden from rsync so they will be deleted in the target container if
+  # they exist. This will allow them to be re-created in the container if
+  # necessary.
   kube::build::rsync \
     --delete \
-    --filter='- /.git/' \
+    --filter='H /.git/' \
     --filter='- /.make/' \
     --filter='- /_tmp/' \
     --filter='- /_output/' \
     --filter='- /' \
-    --filter='- zz_generated.*' \
-    --filter='- generated.proto' \
+    --filter='H zz_generated.*' \
+    --filter='H generated.proto' \
     "${KUBE_ROOT}/" "rsync://k8s@${KUBE_RSYNC_ADDR}/k8s/"
 
   kube::build::stop_rsyncd_container
@@ -714,6 +716,7 @@ function kube::build::copy_output() {
   # We are looking to copy out all of the built binaries along with various
   # generated files.
   kube::build::rsync \
+    --prune-empty-dirs \
     --filter='- /_temp/' \
     --filter='+ /vendor/' \
     --filter='+ /Godeps/' \