diff --git a/sdk-platform-java/hermetic_build/library_generation/postprocess_library.sh b/sdk-platform-java/hermetic_build/library_generation/postprocess_library.sh
index ccd48aac7407..a07d35b362a5 100755
--- a/sdk-platform-java/hermetic_build/library_generation/postprocess_library.sh
+++ b/sdk-platform-java/hermetic_build/library_generation/postprocess_library.sh
@@ -85,11 +85,20 @@ preprocessed_libraries_binding="${owlbot_cli_source_folder}"
 
 pushd "${postprocessing_target}"
 
+# Backs up all files matching `stub/Version.java`
+# This is a workaround to prevent owl-bot-copy from omitting
+# Version.java files when transferring the generated code
+backup_dir=$(mktemp -d)
+backup_version_java "${PWD}" "${backup_dir}"
+
 owl-bot copy-code \
   --source-repo-commit-hash=none \
   --source-repo="${owlbot_cli_source_folder}" \
   --config-file="${owlbot_yaml_relative_path}"
 
+restore_version_java "${PWD}" "${backup_dir}"
+rm -rf "${backup_dir}"
+
 
 # clean the custom owlbot yaml
 if [[ "${is_monorepo}" == "true" ]]; then
diff --git a/sdk-platform-java/hermetic_build/library_generation/templates/owlbot.yaml.monorepo.j2 b/sdk-platform-java/hermetic_build/library_generation/templates/owlbot.yaml.monorepo.j2
index 694a3bf6421d..9ed63c4260b0 100644
--- a/sdk-platform-java/hermetic_build/library_generation/templates/owlbot.yaml.monorepo.j2
+++ b/sdk-platform-java/hermetic_build/library_generation/templates/owlbot.yaml.monorepo.j2
@@ -21,7 +21,6 @@ deep-remove-regex:
 
 deep-preserve-regex:
 - "/{{ module_name }}/google-.*/src/test/java/com/google/cloud/.*/v.*/it/IT.*Test.java"
-- "/.*google-.*/src/main/java/.*/stub/Version.java"
 
 deep-copy-regex:
 - source: "/{{ proto_path }}/(v.*)/.*-java/proto-google-.*/src"
diff --git a/sdk-platform-java/hermetic_build/library_generation/tests/generate_library_unit_tests.sh b/sdk-platform-java/hermetic_build/library_generation/tests/generate_library_unit_tests.sh
index 1a916623bd79..5c973605adb9 100755
--- a/sdk-platform-java/hermetic_build/library_generation/tests/generate_library_unit_tests.sh
+++ b/sdk-platform-java/hermetic_build/library_generation/tests/generate_library_unit_tests.sh
@@ -213,6 +213,27 @@ get_proto_path_from_preprocessed_sources_multiple_proto_dirs_fails() {
   assertEquals 1 ${res}
 }
 
+backup_and_restore_version_java_succeeds() {
+  local target_dir=$(mktemp -d)
+  local backup_dir=$(mktemp -d)
+  
+  mkdir -p "${target_dir}/google-cloud-test/src/main/java/com/google/cloud/test/v1/stub"
+  echo "version1" > "${target_dir}/google-cloud-test/src/main/java/com/google/cloud/test/v1/stub/Version.java"
+
+  backup_version_java "${target_dir}" "${backup_dir}"
+
+  # Simulate owl-bot overwriting the file
+  echo "version2" > "${target_dir}/google-cloud-test/src/main/java/com/google/cloud/test/v1/stub/Version.java"
+
+  restore_version_java "${target_dir}" "${backup_dir}"
+
+  # The original "version1" should have been restored
+  local restored_content=$(cat "${target_dir}/google-cloud-test/src/main/java/com/google/cloud/test/v1/stub/Version.java")
+  assertEquals "version1" "${restored_content}"
+
+  rm -rf "${target_dir}" "${backup_dir}"
+}
+
 normalize_owlbot_yaml_test() {
   local temp_dir=$(mktemp -d)
   local input_file="${temp_dir}/input.yaml"
@@ -266,6 +287,7 @@ test_list=(
   get_proto_path_from_preprocessed_sources_valid_library_succeeds
   get_proto_path_from_preprocessed_sources_empty_library_fails
   get_proto_path_from_preprocessed_sources_multiple_proto_dirs_fails
+  backup_and_restore_version_java_succeeds
   normalize_owlbot_yaml_test
 )
 
diff --git a/sdk-platform-java/hermetic_build/library_generation/tests/resources/goldens/.OwlBot-hermetic-golden.yaml b/sdk-platform-java/hermetic_build/library_generation/tests/resources/goldens/.OwlBot-hermetic-golden.yaml
index e8b942f0dddb..225b4620bf5f 100644
--- a/sdk-platform-java/hermetic_build/library_generation/tests/resources/goldens/.OwlBot-hermetic-golden.yaml
+++ b/sdk-platform-java/hermetic_build/library_generation/tests/resources/goldens/.OwlBot-hermetic-golden.yaml
@@ -21,7 +21,6 @@ deep-remove-regex:
 
 deep-preserve-regex:
 - "/java-bare-metal-solution/google-.*/src/test/java/com/google/cloud/.*/v.*/it/IT.*Test.java"
-- "/.*google-.*/src/main/java/.*/stub/Version.java"
 
 deep-copy-regex:
 - source: "/google/cloud/baremetalsolution/(v.*)/.*-java/proto-google-.*/src"
diff --git a/sdk-platform-java/hermetic_build/library_generation/utils/utilities.sh b/sdk-platform-java/hermetic_build/library_generation/utils/utilities.sh
index 49c121b41f5b..8dcf799f86be 100755
--- a/sdk-platform-java/hermetic_build/library_generation/utils/utilities.sh
+++ b/sdk-platform-java/hermetic_build/library_generation/utils/utilities.sh
@@ -334,6 +334,45 @@ error_if_not_exists() {
   fi
 }
 
+# Backups existing Version.java files in the specified target directory
+# Arguments:
+# 1 - target_directory: The directory where to search for Version.java
+# 2 - backup_directory: The directory where the backups will be stored
+backup_version_java() {
+  local target_directory=$1
+  local backup_directory=$2
+
+  pushd "${target_directory}" > /dev/null
+  find . -type f -path "*/src/*/stub/Version.java" -print0 | while IFS= read -r -d '' file; do
+    local backup_path="${backup_directory}/${file#./}"
+    mkdir -p "$(dirname "${backup_path}")"
+    cp "$file" "${backup_path}"
+  done
+  popd > /dev/null
+}
+
+# Restores Version.java files from the backup directory to the target directory
+# Arguments:
+# 1 - target_directory: The directory where to restore Version.java
+# 2 - backup_directory: The directory where the backups are stored
+restore_version_java() {
+  local target_directory=$1
+  local backup_directory=$2
+
+  if [[ ! -d "${backup_directory}" ]]; then
+    return 0
+  fi
+
+  pushd "${backup_directory}" > /dev/null
+  find . -type f -print0 | while IFS= read -r -d '' file; do
+    local relative_path="${file#./}"
+    local target_path="${target_directory}/${relative_path}"
+    mkdir -p "$(dirname "${target_path}")"
+    mv "$file" "${target_path}"
+  done
+  popd > /dev/null
+}
+
 normalize_owlbot_yaml() {
   local input_file="$1"
   local output_file="$2"